RetrogeneDB ID: retro_pvam_1429

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_8389:28551..29318(-)
• 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_1429
GTAATAGCACTGAAAGCCAGTGGTATACAGGCACATATGACAAAGCAACAGGAGCAGAAGAACCTCAGAAATTTATACAT
ATCAAACTTCCCACTCACAATGAATGAGCAAGAACTAGGGAGAATTCTGAAGCCCTTTGGCTAGGTTATCTCCACTTGAA
CCCTTTGAAACATCAATGGGACCAGCAGAGGGGGTGGCTTTGCCAGGATGGAGTCCACAGAGAAGTACGATGCCATCATG
AACCCCTTTAATGAAAAATATATTAAAACACCCCTGGAGTACCAAGCCCATCTGATCCACTGCTTTGCAAATTTGCTGAT
GGTGTTCTAAAGAAATGACAGGATCAAGAAAAATCTGTGCAAAATTGACAGGCCTAGCCAAGGAATGGAGACATGGTGAT
ATGGCCTTGACCTATGGCCCCACCACAGCTCTTCAGAATTTTACCCAGCTCCCTATAACATCACACCCAAAAGGATGCTT
GCTCAGTCTGTAGTCTCTCCACATCGTCCATCTCCTGAGCCTTCCTACCAGATAGTAACTCAGACAACTCCTCTACAAGT
ACCTAACTTATCTTGGATGCACCACCAGTCATACTTCATGTAGACTTCAGGTTCATTTCTGACACCAGGGATGAATCACC
TCATTTTTCTCCAGCTTGCCTCCATGATGGGACTTCTTACCCAGCAACTGTACCACTTTTCCCTTAGCACCACAGCATGT
ATATGCCAACAGCTGTAGCTACACAAGGAGCTTACATCCCCCAGTAC

Alignment

ORF - retro_pvam_1429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.61 %
• Parental protein coverage: 63.05 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VTALKASGVQAQMAKQQEQ-DPTNLYISNLPLSMDEQELEGMLKPFGQVISTRILRDTSGTSRGVGFARM
          V.ALKASG.QA.M.KQQEQ....NLYISN.PL.M.EQEL...LKPFG.VIST..L....GTSRG.GFARM
Retrocopy VIALKASGIQAHMTKQQEQKNLRNLYISNFPLTMNEQELGRILKPFG*VIST*TL*NINGTSRGGGFARM

Parental  ESTEKCEAIITHFNGKYIKTP-PGIPAPSDPLLCKFADGGPKKRQNQGKFVQNGPAWPRNGDM-GSMALT
          ESTEK..AI...FN.KYIKTP.PG.P.PSDPLLCKFADG..KK.Q.Q.K.VQN..A.PRNGDM.G.MALT
Retrocopy ESTEKYDAIMNPFNEKYIKTP<PGVPSPSDPLLCKFADGVLKK*QDQEKSVQN*QA*PRNGDM<GDMALT

Parental  YDPITALQNGFYPAP-YNITPNRMLAQSTLSPYLPSPVSSYQRVTQTS-LQVPNSSWMHHQSYLMQPSGS
          Y.P.TALQN.F...P.YNITP.RMLAQS..SP..PSP..SYQ.VTQT..LQVPN.SWMHHQSY.M..SGS
Retrocopy YGPTTALQN-FTQLP<YNITPKRMLAQSVVSPHRPSPEPSYQIVTQTTPLQVPNLSWMHHQSYFM*TSGS

Parental  VLTPGMDHRISLQPASMMGPLTQQLGHLSLSTT-GTYMPTATAVQGAYISQY
          .LTPGM.H.I.LQ.ASMMG.LTQQL.H.SLSTT...YMPTA.A.QGAYI.QY
Retrocopy FLTPGMNHLIFLQLASMMGLLTQQLYHFSLSTT<SMYMPTAVATQGAYIPQY

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_1429 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,