I have now observed 3 copies(partials) of this large ORF.
It doesn’t appear to be a transposon, when doing blastn or blastp searches and in one case it appears to get incorporated into the transcripts generated from a gene on the opposite strand.
The ORFeome project have managed to pull this out of their EST library for 2 of them.
If this is a coding gene then there is 1 fully copy that can be annotated as a CDS, 1 Pseudocopy (ORF is split into 2 with no high scoring splice sites) that can be annotated as a pseudogene and 1 truncated copy that also can be annotated as a CDS (or should it).
I was wondering if anyone had any additional ideas as to what it may be?
Sequences are:
GGGCTTGGTGGGACCACCTGGGGCAGCAACAAGGAACTCATGCTTACCACGTTCAAAGCCATCACC
AAACCGGGCGCCACCTACGCCTGCCAAAGTTGGTCTCAACTCGTGAAGCCCACGAGGATATACAGC
CTTGACTCATCGTACAAGGCAATCCTACGCGTCTGCTGCGGCCTCACAAAAAACACCCCTGGATACC
ACATCCACGACGAGGCTGGTATCCTTCCCTTATCCCACGAAATTAAGCTCATGAACCAGCAATATGCA
ATATCCATGATGAAATCTGCGGGTCATCCGTCAAACGGTCTAACAGGCCGTAGAAAGATGGCACGTA
ACACGACAAGAAGTAGCAAGCCGCCCAGGGAACCCCCGCTGGACTTCCCCGCCAAGACACTAGACG
ACTGGAAGAACCACCCAGGCTCCACAAAAAGCCTGCAGAAACTAAACCACACAAAATTCGTTGCTCA
CTTCCTGGCGAACCGACCGTCGAACAAAATACTAGGAATTGCTGCATCAAAAGTCTGCAAATCAGAG
GAAGAGCTCCCTCGTGAAACCCGGACTGAGCTCGCCAGACTGCGTTGTGGCCACTCAAGATTATG
TGGTGCTTACGTTGCCAAAATTGAAAATAGAAGCATTTCCCCTTGCAGGAAATATGGAAGTGTGGAGG
GTGACGTGAATCACCTTTTGACCTGCATCTCCTCGGTCCCCCTACTCCCGAAGGACCTGTGGGAGAAG
CCGATGGAAGTGGCCGAGGCCTCCACGACCCCCTTCGACCCCGGAGGAAACGGAACCACCCCTCCA
AAAGGACTCGCCGGGACCACCTGGGGCAGCAACAAGGAACTCATGCTTACCACGTTCAAAGCCATCA
CCAAACCGGGCGCCACCTACGCCTGCCAAAGTTGGTCTCAACTTGTGAAGCCCACGAGGATGGACAG
CCTTGACTCATCGTACAGGGCAATCCTGCGCGTCTGCTGCGGCCTCACAAAAGACACCCCTGGATACC
ACATCCACGACGAGGCGGGCATCCTTCCCTTATCCCACAAAATTAAGCTCATGAACCAGCAATATGCG
ATATCCATGATAAAATCTGCGGGACATCCATCAAACGGTCTAACAGGCCGCAGAAAGTTGGCACGCAA
CACGACAAGAAGTAGCAAGCCGCCCAGGGAACCCCCGCTGGATTTCCCTGACAAGACACTAGACGAC
TGGAAGAATCACCCTGGCTCCACAAAAAGCCTGCAGAAACTAAACCACACAAAATTCGTTGCTCACTTC
CTGGCGAACCGACCGACGAACAAAATACTAGGAACTGCTGCACCAAAAATCTGCAAATCGGAGGAAG
AGCTCCCTCGTGAAACCCGGACTGAGCTTGCCAGATTGCGCTGTGGCCACTCAAGATTATGTGGTTCT
TACGTTGCCAGAATTGAAAACAGAAGCATTTCCCCTTGCAGGAAATGTGGAAGTGTGGAGGGTGACGT
GAATCACCTTTTGACCTGCATCTCCTCGGTCCCTCTGCTCCCAAAGGACCTGTGGGAGAAGCCGGTGG
AAGTGGCCGAGGCCCTGGGCCTCTCCACGACCCCCTTCGACCCCGGAGGAAACGGAACCACCCCTCCA
TGGAGCTAGCAAGGCTGAGATGTGGACATTCCACGATGGTACCCGGCTACTTCGCGATACCGACCTG
TGGGAAATGTGGCGATCAAAGAGGAAATGTGGCACACTTGTTGGGATGCTCAACCCAACCCCCGCTA
ACGCCATCAAAATTGTGGTCGGATCCGAAAACGGTGGCTGAGGCCCTGGGCCTCCCCACCAAAATAT
TCGACCCTCCGCACCTGCAGTGGTCTCACCAGTGATTCTCCGACTCAGCACATCTATGAGGAAACGGA
GAGGCTTCCTCTTCGCGAGGAAATTGAGCTCCGCAAGCAGCAATTTGCAATTGCAGCACTGAACACCC
CTGGCCACCCATCCAAAGACCTAAAGGCAAGAAGACCCCTTGAGAGGACGACCAACAGGCCCAGAGA
GCCGCCGTTAGACTATCCGAGCAGCACCACCAATGCCTGGACAAATCCCCGCTCAACGACCAAGGCC
ATTCAGAAGTCCAACCACCGAACCTTCATCAAAAACTTCCTAAACAGCAAGAAGCCGAACAACGTACT
TGGACGCCCTGCCCCCGCCATAAATGGTGAGGAAAGCTCCTTGCCGCGAGGAACAAGAGTGGAGCTA
GCCAGAATCAGATGCGGTCACTCAACCATGGTCCCAAGCTATTTCGCGAGAATCAACAACGACACGGT
GCCAGCCTGCAAGAAGTGTGGCGATGTCACAGGGAATGTGGAACACATGCTGAGATGTTCTATCCAA
CCCCCGCTCACTCCGAAAAAGGTGGCAGAGGCACTGGGCCTCCCCACCAGAACTTTCGATCCAGGCG
GATCTCAA
[tr][td]Sequence[/td][td]High Score[/td][td]E-value [/td][td]Num. of HSPs[/td][/tr]
[tr][td]Y64G10A[/td][td]3885[/td][td]1.9e-169[/td][td]1[/td][/tr]
[tr][td]M28[/td][td]3345 [/td][td]4.4e-145[/td][td]2[/td][/tr]
[tr][td]Y56A3A [/td][td]3345[/td][td]5.0e-145 [/td][td]2[/td][/tr]