RetrogeneDB ID: retro_pabe_1769

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:28052326..28053565(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EWSR1
• Ensembl ID: ENSPPYG00000011684
• Aliases: None
• Description: EWS RNA-binding protein 1 [Source:HGNC Symbol;Acc:3508]

Sequence

>retro_pabe_1769
CCTCCCACTAGTTACCCACCCCAAACTTGATCCTACAGCCAAGCTCCAAGTCAGTATAGCTAACAGAGCAGCAGCTACGG
GCAGCAGAGTTCATTCTGACAGGACCACCCCAGTAGCATGGGTGTTTATGGGCAGGAGTCTGGAGGATTTTCCGGACCAG
GAGAGAACCAGAGCATGAGTGGCCCTGACAACTGGGGCAGGGGAAGAGGGGGATTTGATCGTGGAGGCATGAGCAGAGGT
GGGCGGGGAGGAGGATGCGGTGGAATGGGCAGCGCTGGAGAGCGAGGTGGCTTCAATAAGCCTGGTGGACCCATGGATGA
AGGACCAGATCTTGATCTAGGCTCACCTGTAGATCCAGATGAAGACTCTGACAACAGTGCAGTTTATGTACAAGGATTAA
ATGACAATGTGACTCTAGATGATCTGGTAGACTTCTTTAAGCAGTGTGGGGTTGTTAAGATGAACAAGAGAACTGGGCAA
CCCATGATCCACACCTACCTGGACAAGGAAACAAGAAAGCCCAAAGGCGATGCCACAGTGTCCTGTGAAGACCCACCTAC
TGCCAAAGCTGCCGTGGAATGGTTTGATGGGAAAGATTTTCAAGGGAGCAAACTTAAAGTCTCTCTTGCTCGGAAGAGGC
CTCCAATGAACAGTATGCGGGATGGGATGCCACCACCACTCTGCGGAGGTCCAGGAGGCCCAGGAAGTCCTGGGGGACCC
ATGGGTCACATGGGAGGCAGTGGAGGAGATAGAGGAGGCCTCCCTCCAAGAGGACCCCGGAGTTCCCGAGGGAACCCCTC
TGGAGGAGGAAACATCCAGCACCAAGCTGGAGACTGGCAGTGTCCCAATCTGGGTTGTGGAAACCAGAACTTCGCCTGGA
GAACAGAGTGCAACAAGTGTAAGGCCCCAAAGCCTGAAGACTTCCTCCCGCCACCCTTCCTGCCCCCGGGTGGTGATCAT
GGCAGAGGTGGCCCTGGTGGCATGCGGGGAGGGAGAGGTGGCCTCATGGATCATGGTGGTCCCGGTGGAATGTTCAGAGG
TGGCTGTGGTAGAGACAGAGGTGGCTTCCATGGTGGCTGGGGCATGGACCGAGGTGGCTTTGGTGGAGGAAGACGAGGTG
GCCCTGGGGGTCCCCCTGGACGTTTGATGTAACCAATGGGAGGAAGAAGAGGAGGACGTGGAGGACCTGGAAAAATGGAT
AAAGGCGAGCACCGTCAGGAGCGCAGAGATCGGCCCTAC

Alignment

ORF - retro_pabe_1769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.94 %
• Parental protein coverage: 63.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRG
          PPTSYPPQT.SYSQAPSQYS.QSSSYGQQSSF.QDHPSSMGVYGQESGGFSGPGEN.SMSGPDN.GRGRG
Retrocopy PPTSYPPQT*SYSQAPSQYS*QSSSYGQQSSF*QDHPSSMGVYGQESGGFSGPGENQSMSGPDNWGRGRG

Parental  GFDRGGMSRGGRGGGRGGMG-AGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLNDSVTLD
          GFDRGGMSRGGRGGG.GGMG.AGERGGFNKPGGPMDEGPDLDLG.PVDPDEDSDNSA.YVQGLND.VTLD
Retrocopy GFDRGGMSRGGRGGGCGGMGSAGERGGFNKPGGPMDEGPDLDLGSPVDPDEDSDNSAVYVQGLNDNVTLD

Parental  DLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA
          DL.DFFKQCGVVKMNKRTGQPMIH.YLDKET.KPKGDATVS.EDPPTAKAAVEWFDGKDFQGSKLKVSLA
Retrocopy DLVDFFKQCGVVKMNKRTGQPMIHTYLDKETRKPKGDATVSCEDPPTAKAAVEWFDGKDFQGSKLKVSLA

Parental  RKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGNV
          RK.PPMNSMR.GMPP....G...P..G.PGGP.G..G..G..G.RGG.....PPRGPR.SRGNPSGGGN.
Retrocopy RKRPPMNSMRDGMPPPLCGGPGGP--GSPGGPMGHMGGSG--GDRGG----LPPRGPRSSRGNPSGGGNI

Parental  QHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGDRGRGGPGGMRGGRGGLMDRGGPG
          QH.AGDWQCPN.GCGNQNFAWRTECN.CKAPKPE.FLPPPF.PPGGD.GRGGPGGMRGGRGGLMD.GGPG
Retrocopy QHQAGDWQCPNLGCGNQNFAWRTECNKCKAPKPEDFLPPPFLPPGGDHGRGGPGGMRGGRGGLMDHGGPG

Parental  GMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGKMDKGEHRQERRDRP
          GMFRGG.G.DRGGF.GG.GMDRGGFGGGRRGGPGGPPG.LM..MGGRRGGRGGPGKMDKGEHRQERRDRP
Retrocopy GMFRGGCGRDRGGFHGGWGMDRGGFGGGRRGGPGGPPGRLM*PMGGRRGGRGGPGKMDKGEHRQERRDRP

Parental  Y
          Y
Retrocopy Y

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	1.44 RPM	151.22 RPM
SRP007412_cerebellum	0.12 RPM	171.58 RPM
SRP007412_heart	0.30 RPM	70.62 RPM
SRP007412_kidney	0.89 RPM	154.43 RPM
SRP007412_liver	0.31 RPM	97.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1769 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1769 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1769 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008298	2 retrocopies	retro_amel_191, retro_amel_959,
Canis familiaris	ENSCAFG00000012160	8 retrocopies	retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560,
Callithrix jacchus	ENSCJAG00000019987	4 retrocopies	retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911,
Homo sapiens	ENSG00000182944	1 retrocopy	retro_hsap_463,
Gorilla gorilla	ENSGGOG00000012212	1 retrocopy	retro_ggor_444,
Macropus eugenii	ENSMEUG00000008703	1 retrocopy	retro_meug_1424,
Myotis lucifugus	ENSMLUG00000012058	1 retrocopy	retro_mluc_328,
Monodelphis domestica	ENSMODG00000008679	1 retrocopy	retro_mdom_279,
Oryctolagus cuniculus	ENSOCUG00000004432	2 retrocopies	retro_ocun_1346, retro_ocun_242,
Pongo abelii	ENSPPYG00000011684	1 retrocopy	retro_pabe_1769 ,
Pan troglodytes	ENSPTRG00000014218	1 retrocopy	retro_ptro_350,
Ictidomys tridecemlineatus	ENSSTOG00000023177	1 retrocopy	retro_itri_1892,
Tursiops truncatus	ENSTTRG00000011881	1 retrocopy	retro_ttru_1366,