RetrogeneDB ID: retro_ptro_350

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:144624833..144626028(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EWSR1
• Ensembl ID: ENSPTRG00000014218
• Aliases: None
• Description: Ewing sarcoma breakpoint region 1 [Source:UniProtKB/TrEMBL;Acc:K7AX24]

Sequence

>retro_ptro_350
CCTCCCACTAGTTACCCACCCCAAACTTGATCCTACAGCCAAGCTCCAAGTCAGTATAGCTAACAGAGCAGCAGCTACGG
GCAGCAGAGTTCATTCTGACAGGACCACCCCAGTAGCATGGGTGTTTATGGGCAGGAGTCTGGAGGATTTTCCGGACTAG
GAGAGAACCGGAGCATGAGTGGCCCTGATAACTGGGGCAGGGGAAGAGGGGGATTTGATCGTGGAGGCATGAGCAGAGGT
GGGTGGGGAGGAGGATGCGGTGGAATGGGCAGTGCTGGAGAGCAAGGTGGCTTCAATAAGCCTGGTGGACCCATGGATGA
AGGACCAGATCTTGATCTAGGCCCACCTGTAGATCCAGATGAAGACTCTGACAACAGTGCAATTTATGTACAAGGATTAA
ATGACAATGTGACTCCAGATGATCTGGTAGACTTCTTTAAGCAGTGTGGGGTTGTTAAGATGAACAAGAGAACTGGGCAA
CCCATGATCCACACCTACCTGGACAAGGAAACAAGAAAGCCCAAAGGTGATGCCACAGTGTCCTGTGAAGACCCACCTAC
TGCCAAAGCTGCCGTGGAATGGTTTGATGGGAAAGATTTTCAAGGGAGCAAACTTAAAGTCTCTCTTGCTCGGAAGAGGC
CTCCAGTGAACAGTATGCAGGGTGGTATGCCACCCCGTGAGGGCAGAGGGATGCCACCACCACTCTGCGGAGGTCCAGGA
GGCCCAGGAAGTCCTGGGGGACCCATGGGTCACATGGGAGGCCGTGGAGGAGATAGAGGAGGCCTCCCTCCAAGAGGACC
CCAGGGTTCCCGAGGGAACACCTCTGGAGGAGGAAACGCCCAGCACCAAGCTGGAGACAGGCAGTGTCCCAATCCGGGTT
GTGGAAACCAGAACTTCGCCTGGAGAACAGAGTGCAACAAGTGTAAGGCCCCAAAGCCTGAAGGCTTCCTCCCGCCACCC
TTCCCACCCCCGGGTGGTGATCATGGCAGAGGTGGCCCTGGTGGCATGCGGGGAGGAAGAGGTGGCCTCATGGATCATGG
TGGTCCTGGTGGAATGTTCAGAGGTGGCTGTGGTAGAGACAGAGGTGGCTTCCGTGGTGGCTGGGCATGGACCGAGGTGG
CTTTGGTGGAGGAAGACAAGGTGGCCCTGGGGGGCCCCCTAGACCTTTGATGTAACCAATGGAGGAAGAAGAGGA

Alignment

ORF - retro_ptro_350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.52 %
• Parental protein coverage: 60.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRG
          PPTSYPPQT.SYSQAPSQYS.QSSSYGQQSSF.QDHPSSMGVYGQESGGFSG.GENRSMSGPDN.GRGRG
Retrocopy PPTSYPPQT*SYSQAPSQYS*QSSSYGQQSSF*QDHPSSMGVYGQESGGFSGLGENRSMSGPDNWGRGRG

Parental  GFDRGGMSRGGRGGGRGGMGSAGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLNDSVTLD
          GFDRGGMSRGG.GGG.GGMGSAGE.GGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLND.VT.D
Retrocopy GFDRGGMSRGGWGGGCGGMGSAGEQGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLNDNVTPD

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

Parental  RKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGNV
          RK.PP.NSM.GGMPPREGRGMPPPL.GGPGGPG.PGGPMG.MGGRGGDRGG.PPRGP.GSRGN.SGGGN.
Retrocopy RKRPPVNSMQGGMPPREGRGMPPPLCGGPGGPGSPGGPMGHMGGRGGDRGGLPPRGPQGSRGNTSGGGNA

Parental  QHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGDRGRGGPGGMRGGRGGLMDRGGPG
          QH.AGD.QCPNPGCGNQNFAWRTECN.CKAPKPEGFLPPPFPPPGGD.GRGGPGGMRGGRGGLMD.GGPG
Retrocopy QHQAGDRQCPNPGCGNQNFAWRTECNKCKAPKPEGFLPPPFPPPGGDHGRGGPGGMRGGRGGLMDHGGPG

Parental  GMFRGGRGGDRGGFRGG-RGMDRGGFGGGRRGGPGGPPGPLMEQM-GGRRG
          GMFRGG.G.DRGGFRGG..GMDRGGFGGGR.GGPGGPP.PLM..M.GGRRG
Retrocopy GMFRGGCGRDRGGFRGG<LGMDRGGFGGGRQGGPGGPPRPLM*PM<GGRRG

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	0.48 RPM	124.87 RPM
SRP007412_cerebellum	0.25 RPM	219.75 RPM
SRP007412_heart	0.23 RPM	90.91 RPM
SRP007412_kidney	0.05 RPM	155.81 RPM
SRP007412_liver	0.07 RPM	189.30 RPM
SRP007412_testis	0.11 RPM	438.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_350 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_350 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_463
Gorilla gorilla	retro_ggor_444

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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,