RetrogeneDB ID: retro_amel_454

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192450.1:1462607..1463824(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMS2
• Ensembl ID: ENSAMEG00000004054
• Aliases: None
• Description: RNA binding motif, single stranded interacting protein 2 [Source:HGNC Symbol;Acc:9909]

Sequence

>retro_amel_454
CTGCTCTCAGTGATTTCCAGGCATGGGATTTTGACTTTTGGTTATAACAAAAACAAGAAGCTGTATGTGTCATTCATTGC
CTCATCATATGGCATCACCTAGTCCAAGCAATAGTACCCCCAGGAGCAGCAGTGGGATTTTGGAAATGACCAGCTGAGCA
AAACCAACCTCCATATCCAGGGGTTGCAACCAGGCATTACTGACCAGGACCCTGTCAAATTGTACCAGTCCTATGGCGAG
GTTGTCTCCACCAAGGTCATACTGGACAAGAGCACGAACAAATGCAAAGGCTATGGTTTTGTGAACTTTGACAGTCCTTC
AGCAGCACAATAAGCTGTTAACAGTACTGAAAGCCAGCAGCTTACAGGCACAAATGATAAAGCAACAGGAACAGGACCCC
ACAAGTTTATACCTACCAAACCTTCCACTAGCAATAGATAAGCAAGAACTGGGAGGGGATGCTGAAGCCCTTTGGCCAGG
TTATCTCCACTGGAATCCTCAGAGACACCAGTGGGACCAGCAGAGGGATTGGCTGTGCAAGAAATGAGTCCACAGAGAAG
TGTGAAGCCATCATCACCCATTTTAATGGAAAACATATTAAAGCACCTGCTGGAATACCAGCTCCATCTGATCCCTTGCT
TTGCAAATTTGCTGATGGTGGTCCAAAGAAATGTCAGAACCAAGGATAATCTTTGCAAAATGGACAGGCCTGGCCAAGGA
ATGCAGATGCAAGTGGTATAGCCTTGACCTATGACCCCACCATAGCTCTTCCAAATGGGTTCCCCAGCTCCTTATAACAT
CACCCCCAACAGGATGCTTGCTTAGTCTACACTCTCCCCCTATCTTACATCTCCTGTGTCTTCAAATGAGAGAGTGACTC
AGACATCTCTTCTACAAGCACCTAATCCATCTTGGATACACCACCAATTATATCTCATGCAGCCTTCAGCTTCAGTTCTG
TCACCTGGGATGGATCACCCCATTTCTCACCAGCCTGCCTGCATGGTGGGACCTCTTACCCAGCAGATGGGTCACCACTT
CCTCAGCAGCTCAGACACATACATGCCCATGGCTGCCACTACGCAAGGAGCTCACATCTCCCAGTACCCCCTGTGCCTTC
TGCTAGTGTTTCAGCAGAGGGGAGCAGTGGCCAGCAACATCAAGTTTTGCTGGATGCTTCCTCAGACAATGGGGTTTACT
CTTTCCAGTTCAACAAG

Alignment

ORF - retro_amel_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.79 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LLSVTSRPGISTFGYN-KNNKKPYVSLSQQMAPPSPSNSTPNSSNG-SNGNDQLSKTNLYIRGLQPGTTD
          LLSV.SR.GI.TFGYN.K.......SL...MA.PSPSNSTP.SS.G...GNDQLSKTNL.I.GLQPG.TD
Retrocopy LLSVISRHGILTFGYN>KTRSCMCHSLPHHMASPSPSNSTPRSSSG<DFGNDQLSKTNLHIQGLQPGITD

Parental  QDLVKLCQSYGKIVSTKAILDKSTNKCKGYGFVDFDSPSAAQ-KAVTALKASGVQAQMAKQQEQDPTNLY
          QD.VKL.QSYG..VSTK.ILDKSTNKCKGYGFV.FDSPSAAQ.K..T.LKAS..QAQM.KQQEQDPT.LY
Retrocopy QDPVKLYQSYGEVVSTKVILDKSTNKCKGYGFVNFDSPSAAQ>KLLTVLKASSLQAQMIKQQEQDPTSLY

Parental  ISNLPLSMDEQEL-EGMLKPFGQVISTRILRDTRGTSRGVGFARMESTEKCEAIITHFNGKYIKTPAGVP
          ..NLPL..D.QEL.EGMLKPFGQVIST.ILRDT.GTSRG.G.AR.ESTEKCEAIITHFNGK.IK.PAG.P
Retrocopy LPNLPLAIDKQEL>EGMLKPFGQVISTGILRDTSGTSRGIGCARNESTEKCEAIITHFNGKHIKAPAGIP

Parental  APSDPLLCKFADGGPKKRQNQGKYMQNGRAWPRNGDMGGMALTYDPTTALQNGFYPA-PYNMTPNRMLAQ
          APSDPLLCKFADGGPKK.QNQG...QNG.AWPRN.D..G.ALTYDPT.AL.NGF.P..PYN.TPNRMLA.
Retrocopy APSDPLLCKFADGGPKKCQNQG*SLQNGQAWPRNADASGIALTYDPTIALPNGF-PS>PYNITPNRMLA*

Parental  SALSPYLPSPVSSYQRVTQTSPLQVPNPSWTHHPSYLMQPSGSVLPPGMDHPLSLQPASMMGPLTQQLGH
          S.LSPYL.SPVSS..RVTQTS.LQ.PNPSW.HH..YLMQPS.SVL.PGMDHP.S.QPA.M.GPLTQQ.GH
Retrocopy STLSPYLTSPVSSNERVTQTSLLQAPNPSWIHHQLYLMQPSASVLSPGMDHPISHQPACMVGPLTQQMGH

Parental  LSLSSTGTYVPAAAPVPGAYIS-PYTPVPSSGVAAEESSGPQTQVPVDAPSDHGLYSFQFSK
          ..LSS..TY.P.AA...GA.IS.P..PVPS..V.AE.SSG.Q.QV..DA.SD.G.YSFQF.K
Retrocopy HFLSSSDTYMPMAATTQGAHIS<PVPPVPSASVSAEGSSGQQHQVLLDASSDNGVYSFQFNK

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_454 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_454 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Ailuropoda melanoleuca	ENSAMEG00000004054	1 retrocopy	retro_amel_454 ,
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
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,
Rattus norvegicus	ENSRNOG00000003076	1 retrocopy	retro_rnor_1374,
Sus scrofa	ENSSSCG00000000402	1 retrocopy	retro_sscr_546,
Tursiops truncatus	ENSTTRG00000002117	1 retrocopy	retro_ttru_715,