RetrogeneDB ID: retro_itri_1892

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH395471.1:3058..4320(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025301
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EWSR1
• Ensembl ID: ENSSTOG00000023177
• Aliases: None
• Description: EWS RNA-binding protein 1 [Source:HGNC Symbol;Acc:3508]

Sequence

>retro_itri_1892
CCTCCCACTAGTTACCCCCCCCCAGACTGGATCCTATAGCCAGGCTCCAAGTCAATGTAGCCAACAAAGCAGCAGCTACG
CACAGAAGAGTTCATTCCGACAGGACCACCCCAGTAGCATGGGTGTTTATGGGCAGGAGTCTGGAGGATTTTCCTGACCA
GGAGAGAACCGGAGCATGGGTGGCCCTGGTAACCAGGGCAGGGGAAGAGGGGGATTTGATCGTGGAGGCATGAGCAGAGG
TGGGCGGAGAGGAGGATGCGGTGGAATGGGCAGCGCTGGAGAGCGAGGTGGCTTCAATAAGCCTGGAGGACCCATGGATG
AAGGACCAGATCTTGAACTAGGCCCTCCAGTAGATCCTGATGAAGACTCTGACAACAGTGCAGTTTATGTGAAAGGATTA
AATGACAGTGTGACTCTTGATGATCTGTCAGATTTCTTTAAGCAGTGTGGGGTTGTTAAGATGAATAAGAGAACTGGGCA
ACCCATGATCCACATCTACCTGGACAAAGAAACAGGAAAGGACAAAGGTGATGCCACAGTGTCCTATGAAGACCCGCCAA
CTGCCAAGGCTGCTGTGGAGTGGTTTGATGGAAAAGATTTTCAAAGAAGCAAACTAAAAGTCACTCTTGCTCGAAAGAAG
CCTCCCATTAACAGCTTGCGGGGTGGCAAGCCACCTCTTGAGGGCAGAGGGATGCCACCATCACTCCGTGGAGGTCCAGG
TGGCCCAGGAGGTCCTGGGCAACCCATGGGTCGCATGGGAGGCCGTGGAGGAGACAGAGGAGGTTTTCCCCCAAGAGGGC
CACGGAGTTCCACAGGGAATCCCTCTGGAGGAGGAAACGTCCAGCACCGAGCTGGGGACTGGCAATGTCCCAATCCGGGT
TGTGGAAACCAGAACTTCGCCTGGAGAACAGAATGCAACGAGTGTAAGGCCCGAAGCCTGAGGGCTTTCTCCCACCACCT
TTCCCACTCCCTGGGTGGTGACCTTGGAAGAGGTGGCCCTGGTGGTATGCGAGGAGGAAGAGGTGGCCTCATGGACCGTG
GCGGTTTTGGAGGAATGTTCAGGGGTGGCCGTGGTGGAGATGGGTGGCTTCCATGATGGTCGTGGCATGGACCAAGGTGG
CTTTGGCGGCGGAAGTGGAGGTGGTCCAGGGGGTCTCCCTGGACCTTTAATGAAGCAGATGGGAGAAAGAAGAGGTGGAC
ACGGAGGACCTGGAAAAATGGATAAAGGCGAGCACCGTCAGGAACGCAGAGATCGGCCCTAC

Alignment

ORF - retro_itri_1892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.24 %
• Parental protein coverage: 63.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PPTSYPPQ-TGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGR
          PPTS.....TGSYSQAPSQ.SQQSSSY.Q.SSFRQDHPSSMGVYGQESGGFS.PGENRSM.GP.N.GRGR
Retrocopy PPTSXXXX>TGSYSQAPSQCSQQSSSYAQKSSFRQDHPSSMGVYGQESGGFS*PGENRSMGGPGNQGRGR

Parental  GGFDRGGMSRGGRGGGRGGMG-AGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAVYVQGLNDNVTL
          GGFDRGGMSRGGR.GG.GGMG.AGERGGFNKPGGPMDEGPDL.LGPPVDPDEDSDNSAVYV.GLND.VTL
Retrocopy GGFDRGGMSRGGRRGGCGGMGSAGERGGFNKPGGPMDEGPDLELGPPVDPDEDSDNSAVYVKGLNDSVTL

Parental  DDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVTL
          DDL.DFFKQCGVVKMNKRTGQPMIHIYLDKETGK.KGDATVSYEDPPTAKAAVEWFDGKDFQ.SKLKVTL
Retrocopy DDLSDFFKQCGVVKMNKRTGQPMIHIYLDKETGKDKGDATVSYEDPPTAKAAVEWFDGKDFQRSKLKVTL

Parental  ARKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGN
          ARKKPP.NS.RGG.PP.EGRGMPP.LRGGPGGPGGPG.PMGRMGGRGGDRGGFPPRGPR.S.GNPSGGGN
Retrocopy ARKKPPINSLRGGKPPLEGRGMPPSLRGGPGGPGGPGQPMGRMGGRGGDRGGFPPRGPRSSTGNPSGGGN

Parental  VQHRAGDWQCPNPGCGNQNFAWRTECNQCKA-PKPEGFLPPPFPPPG-GDRGRGGPGGMRGGRGGLMDRG
          VQHRAGDWQCPNPGCGNQNFAWRTECN.CKA.PKPEGFLPPPFP.PG.GD.GRGGPGGMRGGRGGLMDRG
Retrocopy VQHRAGDWQCPNPGCGNQNFAWRTECNECKA<PKPEGFLPPPFPLPG>GDLGRGGPGGMRGGRGGLMDRG

Parental  GPGGMFRGGRGG-DRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGKMDKGEHRQER
          G.GGMFR.G..G...GGF..GRGMD.GGFGGG..GGPGG.PGPLM.QMG.RRGG.GGPGKMDKGEHRQER
Retrocopy GFGGMFR-GGRG>EMGGFHDGRGMDQGGFGGGSGGGPGGLPGPLMKQMGERRGGHGGPGKMDKGEHRQER

Parental  RDRPY
          RDRPY
Retrocopy RDRPY

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1892 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1892 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 17 parental genes, and 30 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,
Cavia porcellus	ENSCPOG00000009502	1 retrocopy	retro_cpor_1353,
Felis catus	ENSFCAG00000004243	1 retrocopy	retro_fcat_519,
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,
Mustela putorius furo	ENSMPUG00000013432	2 retrocopies	retro_mputfur_56, retro_mputfur_572,
Mus musculus	ENSMUSG00000009079	1 retrocopy	retro_mmus_1379,
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,