RetrogeneDB ID: retro_pvam_695

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_778:27663..28828(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMS2
• Ensembl ID: ENSPVAG00000007616
• Aliases: None
• Description: RNA binding motif, single stranded interacting protein 2 [Source:HGNC Symbol;Acc:9909]

Sequence

>retro_pvam_695
TTCTGATATAACAAGAACAAAAAGAAGCCAAATGTGTCATTGTCTCAGCAGAAGGCACCACTTAGTCCAAGCAATGGTTC
CCCTAACAGTAGCAGTGTGAGCAATGGAAATGACCAGCTGAGCAAAACTAACTTCTACATCCAGGGATTGCAACCAGGCA
CTATTCAACAGGACCATGTCAAATTGTGTCAGTCATATGGCAAGACTGTCTCCATTATGGCTATACTGGACAAGACCACA
AACAAATGCAAAGGCTATGGCTCTGTGAACTATGACAGTACTTCAGCCATAAAGAAAGCTATAACAGAACTGAAAGCCAG
TGATGTACTGATACAGATGGCACAACAGGAGGAACCCACAAATTTATACATATCAAACCTCCCACTGTCAATGGATGAGC
AAGAACTGGAAGGAATACTGAAGCCCTTTGGCCAGGTTATCTCCACTTGAATCCTTGGAGACACTAGCAGGATCAGCAAA
GGGGTTGGCTTTGCAAGGATGGAGTCCATAAAAAAGTGTGAAGCCATCATCACCCACTTTAATGAAAAATATGTTAAGAC
ACTCCCTGGAGTACCAGCCCCAACATTTTGCTGCTTTGCAAATTTGCTGATGGTGGTCCAAAGAAATGACAGAATCAAGA
AAAACTTATGCAAAATGGATGGGCCTGGCCAAGGATTGGAGATATAGATGGTATGGTATTGACCTATGACCTCACTATAG
CTCTTCTGAATGGGTTTTACCCAGCTCCTTAAAACATCATCCCCAACAGGATGCTTGCTCAGTTTACACTGTCCCTGTAT
CTTCCATCTTCGTGTCTTCATATCAGAAGTAACTCAGACATTTCCTCTACAAGTATCTAACCCATCTTGGATGTAACACC
AGTCATATCTCATGCAGCCTTCAGGTTCAGTTCTGACCCTAGGGATGAATCACCCCATTGCTCTCTAGCCTGCCTTCATG
ATGGGAGCTCTTACCCATCAACTGGGCCACCTCCCTCTGAGCACCTGGGCACATATATGCCAATAGCTGCAGCTATGTAA
GCAGCTTACATCTCCCAGTACACCCTGCGCCTTTACCCAATGTTTCAATTGAGAGCAGCAGCCAGGAAAACCAAGTGATG
GTACATGCTCCCTCAGACCATGGGGTTTATTCTTTCCAGTTCAAC

Alignment

ORF - retro_pvam_695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.87 %
• Parental protein coverage: 96.55 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FGYNKNNKKAYVSLSQQMAPPSPSSSTPNSSNGNNGNDQLSKTNLYIRGLQPGTTDQDLVKLCQSYGKIV
          F.YNKN.KK..VSLSQQ.AP.SPS...PNSS...NGNDQLSKTN.YI.GLQPGT..QD.VKLCQSYGK.V
Retrocopy F*YNKNKKKPNVSLSQQKAPLSPSNGSPNSSSVSNGNDQLSKTNFYIQGLQPGTIQQDHVKLCQSYGKTV

Parental  STKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELEG
          S..AILDKTTNKCKGYG.V..DS.SA..KA.T.LKAS.V..QMA.Q.E..PTNLYISNLPLSMDEQELEG
Retrocopy SIMAILDKTTNKCKGYGSVNYDSTSAIKKAITELKASDVLIQMAQQEE--PTNLYISNLPLSMDEQELEG

Parental  MLKPFGQVISTRILRDTSGTSRGVGFARMESTEKCEAIITHFNGKYIKTPPGIPAP-SDPLLCKFADGGP
          .LKPFGQVIST.IL.DTS..S.GVGFARMES..KCEAIITHFN.KY.KT.PG.PAP....LLCKFADGGP
Retrocopy ILKPFGQVIST*ILGDTSRISKGVGFARMESIKKCEAIITHFNEKYVKTLPGVPAP<NILLLCKFADGGP

Parental  KKRQNQGKFVQNGPAWPRNGDMGSMALTYDPITALQNGFYPAPYNITPNRMLAQSTLSPYLPSP-VSSYQ
          KK.QNQ.K..QNG.AWPR.GD...M.LTYD...AL.NGFYPAP.NI.PNRMLAQ.TLS.YLPS..VSSYQ
Retrocopy KK*QNQEKLMQNGWAWPRIGDIDGMVLTYDLTIALLNGFYPAP*NIIPNRMLAQFTLSLYLPSS<VSSYQ

Parental  R-VTQT-SLQVPNSSWMHHQSYLMQPSGSVLTPGMDHRISLQPASMMGPLTQQLGHLSLST-TGTYMPTA
          ..VTQT..LQV.N.SWM.HQSYLMQPSGSVLT.GM.H.I.L.PA.MMG.LT.QLGHL.LST..GTYMP.A
Retrocopy K<VTQTFPLQVSNPSWM*HQSYLMQPSGSVLTLGMNHPIAL*PAFMMGALTHQLGHLPLST<LGTYMPIA

Parental  TAVQGAYISQYT-PVPSSNVSVEESSGQQNQVTVDAPSDHGVYSFQFN
          .A...AYISQYT.P.P..NVS..ESS.Q.NQV.V.APSDHGVYSFQFN
Retrocopy AAM*AAYISQYT<PAPLPNVSI-ESSSQENQVMVHAPSDHGVYSFQFN

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_695 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004054	1 retrocopy	retro_amel_454,
Callithrix jacchus	ENSCJAG00000010803	1 retrocopy	retro_cjac_1022,
Homo sapiens	ENSG00000076067	1 retrocopy	retro_hsap_1143,
Myotis lucifugus	ENSMLUG00000000530	1 retrocopy	retro_mluc_1093,
Mus musculus	ENSMUSG00000040043	1 retrocopy	retro_mmus_1530,
Pan troglodytes	ENSPTRG00000005104	1 retrocopy	retro_ptro_778,
Pteropus vampyrus	ENSPVAG00000007616	2 retrocopies	retro_pvam_1429, retro_pvam_695 ,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000003076	1 retrocopy	retro_rnor_1374,
Sus scrofa	ENSSSCG00000000402	1 retrocopy	retro_sscr_546,
Tursiops truncatus	ENSTTRG00000002117	1 retrocopy	retro_ttru_715,