RetrogeneDB ID: retro_pvam_203

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1855:161912..162962(+)
• Located in intron of: ENSPVAG00000016087

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSPVAG00000005000
• Aliases: None
• Description: male-specific lethal 3 homolog (Drosophila) [Source:HGNC Symbol;Acc:7370]

Sequence

>retro_pvam_203
ATGGAAGAAAGACTAATACTATAGACATCCCGGATGTTCTGAAGAAGAAACTCGAGGATGACTGTCTATTATATCAACAG
GAGGAAACGGTTAGTGAAACTTCCATGCCAGACCAACATCATAACTATTTTGGAATCCTATGTGAAGCATTTTGCTATCA
ATGCAGCCTTTTCAGCCAGTGAGAGGCCTTATCATCATGCTGTGTCACACACCAACATGAATGTGCATTGCATCCCAGCA
GAAAAGAATGTTGACCTTTGTAAGGAGATGGTGGATGGATTAAGAATAACCTTTGATTACACTCTCCCATTGGTTTTGCT
TTATCCATATGAACAAGCTCAGTATAAAAAGGTGACTTCGTCCAAATTTTTTCCTCCGATTAAGGAAAGTGCCATAAACA
CTAATAGGAACCAGGAGGGACTCTCTCCAAGTCCACCTTTGTTGAATCGGTTCATCCCACAGTCCACGGAGAGTCGGTGT
GAGCTTGCTGCTCCCAAAAGGCGCAAAGCTGAGCCAGAAGCCTTGCAGTCTCTGAGGCGGTCCAGGCGCCACTCTGCCAA
CTGCGACAAGCTGTCTGAGAGCAGTGCCTCGCCTCAGCCCAAGCACCAGCAGCAGGACGTGTCCACCAGCATGCCCAAGC
TGTTCCTGCACCTAGAAAAGAAGACGCCTGTGCATAGCAGACCATCCTCGCCTGTTCCTCTGACCCCAAGCAAGGAAGGC
GGTGGGGTGTTTGCCATCTGTGAAGGCAGAACTAATGAAATAAATGAGGTCCTCTCCTGGGAACTCGTACCCAACAGTTA
CCCACTAGGTGACCAGTCTCTTCCACCCTCCTACATTTATGGGGCACAACACTTGCTGAGATTGTTTGTGAAACTTCCAG
AAATCCTGGTCAAGATGTCCTTTTCGGAGAAGAATCTGAAGGCTTTACTGAAGCACTTTGACCTCTTTCTGAGGTTTTTA
GAAGAGTACCACGACAGCTTCTTCCCAGAGTCTGCCTATGTCACCGCCTGTGAGGCATACAACAGCATTAAGAATCCCAG
GGCAATTTAT

Alignment

ORF - retro_pvam_203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.87 %
• Parental protein coverage: 72.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEERII-TIEIPEVLKKKLEDDC-YYINRRKRLVKLPCQTNIITILESYVKHFAINAAFSAHERPRHHHA
          MEER.I.TI.IP.VLKKKLEDDC.YYINRRKRLVKLPCQTNIITILESYVKHFAINAAFSA.ERP..HHA
Retrocopy MEERLI<TIDIPDVLKKKLEDDC>YYINRRKRLVKLPCQTNIITILESYVKHFAINAAFSASERP-YHHA

Parental  MSHASMNVHYIPAEKNVDLCKEMVDGIRITFDYTLPLVLLYPYEQVQYKKVTSSKFFLPIKESATSTSRN
          .SH..MNVH.IPAEKNVDLCKEMVDG.RITFDYTLPLVLLYPYEQ.QYKKVTSSKFF.PIKESA..T.RN
Retrocopy VSHTNMNVHCIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFPPIKESAINTNRN

Parental  QEELSPSPPLLNPSTPQSTESQPATGEPATPKRRKAEPEALQSLRRSTRHSANCDRLSESSASPQPKRRQ
          QE.LSPSPPLLN...PQSTES.....E.A.PKRRKAEPEALQSLRRS.RHSANCD.LSESSASPQPK..Q
Retrocopy QEGLSPSPPLLNRFIPQSTESR---CELAAPKRRKAEPEALQSLRRSRRHSANCDKLSESSASPQPKHQQ

Parental  QDTSASMPKLFLHLEKKTPVHSRSSSPVPLTPSKEGSTVFASFEGRRTNEINEVLSWKLVPDSYPPGDQP
          QD.S.SMPKLFLHLEKKTPVHSR.SSPVPLTPSKEG..VFA..EG.RTNEINEVLSW.LVP.SYP.GDQ.
Retrocopy QDVSTSMPKLFLHLEKKTPVHSRPSSPVPLTPSKEGGGVFAICEG-RTNEINEVLSWELVPNSYPLGDQS

Parental  PPPSYIY-AQHLLRLFVKLPEILGKMSFSEKNLKALLKHFDLFLRFLAEYHDDFFPESAYVAACEAHYST
          .PPSYIY.AQHLLRLFVKLPEIL.KMSFSEKNLKALLKHFDLFLRFL.EYHD.FFPESAYV.ACEA..S.
Retrocopy LPPSYIYGAQHLLRLFVKLPEILVKMSFSEKNLKALLKHFDLFLRFLEEYHDSFFPESAYVTACEAYNSI

Parental  KNPRAIY
          KNPRAIY
Retrocopy KNPRAIY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_203 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009278	1 retrocopy	retro_btau_883,
Callithrix jacchus	ENSCJAG00000001061	1 retrocopy	retro_cjac_1490,
Cavia porcellus	ENSCPOG00000004692	5 retrocopies	retro_cpor_1423, retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens	ENSG00000005302	2 retrocopies	retro_hsap_2401, retro_hsap_4097,
Gorilla gorilla	ENSGGOG00000006582	2 retrocopies	retro_ggor_1820, retro_ggor_2749,
Macaca mulatta	ENSMMUG00000002689	2 retrocopies	retro_mmul_2362, retro_mmul_972,
Monodelphis domestica	ENSMODG00000017350	1 retrocopy	retro_mdom_1422,
Pongo abelii	ENSPPYG00000020123	2 retrocopies	retro_pabe_2166, retro_pabe_3353,
Pan troglodytes	ENSPTRG00000021662	2 retrocopies	retro_ptro_1751, retro_ptro_2778,
Pteropus vampyrus	ENSPVAG00000005000	1 retrocopy	retro_pvam_203 ,
Sorex araneus	ENSSARG00000008477	1 retrocopy	retro_sara_139,
Tarsius syrichta	ENSTSYG00000012788	4 retrocopies	retro_tsyr_1079, retro_tsyr_1649, retro_tsyr_1706, retro_tsyr_948,