RetrogeneDB ID: retro_amel_191

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192349.1:2525879..2527832(-)
• Located in intron of: ENSAMEG00000005872

Retrocopy information

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

Parental gene information

• Parental gene symbol: EWSR1
• Ensembl ID: ENSAMEG00000008298
• Aliases: None
• Description: EWS RNA-binding protein 1 [Source:HGNC Symbol;Acc:3508]

Sequence

>retro_amel_191
TCCACGGATTACAGTACCTATAGCCAAGCTGCAGCCCAGCCGGGCTACAGTGCACACACCACCCAACCCACTCAAGGATA
TGCACAGACCACCCAGGCATATGCGCAGCAAAGTTATGGAACCTATGGACAGCCCACTGATGTCAGCTATACCCAGGCTC
AGACCACTGCGACCTATGGGCAGACTGCCTATGCAACTTCTTATGGACAGCCTCCCGCTGGTTATACTACTCCAACTGCC
ACCCAGGCATAGAGTCAGCATGTCCAGGGGTATGGCACTGGTGCTTACGATACCACCACTGCTACGGCCACTACCACCCA
GGCCTCCTATGCAGCTCAGTCTGCTTATGGCACTCAGCCTGCTTACTCAGCCTATGGAAAGGAGCCAGCAGCCACCGCAC
CTGAAAGACCACAGGATGGTAACAAACCCGCTGAGACTAGTCAACCTCAATCTAGCACAGGGGGTTACAATCAGCCCAGC
CTAGGATATGGACAGAGTAACTACAGTTATCCCCAGGTACCTGGGAGCTACCCCATGCAGCTAGTCACAGCGCCACCATC
TTACTCTCCTACCAGCTACTCCTCTACACAGACAACTAGTTATGATCAGAGCAGTTACTCTCAGCAAAACACCTATGGGC
AGCCGAGAGCTATGGACAGCAGAGTAGCTATGGTCAAAAAAGCAGCTACGGGCATCAGCCGCCCACTAGTTATCCCCCCT
AAACTGGATCCTACAGCCAGGCTCCAAGTCAATATAGCCAACAGAGCAGCAGCTACGGGCAGCAGAGTTCATTCCAACAG
GACCACCCCAGTAGCATGGGTGTTTATGGGCAGGACTCTGGAGGATTTTCCAGACCAGGAGAGAACCGGGCATGAGTGGT
CCTGATAACGGGGGCAGGGGAAGTGGGGGATTTGGTAGCGGAGGCATGAGCAGAGGTGGGCAGGGAGGAGGACATGGTGG
AATGGGTGCTGGAGAGCGAGGTGTCTTCAATAAGCCTGGTGGACCCACGGACGAAGGACCAGATCTTGATCTAGGCCTAC
GTGTAGATCGAGATGAAGACTCTGACAACAGTGCAGTTCATGTGCAAGGCTGAAATGACAGTGGGACTCTAGATGATCTG
GCCGACTTCTTGAAGCAGTGTGGAGTTGTTAAGATGAACAAGAGAACCGGACAACCCATGATCCATATCTACTTGGACAA
GGAAACAGGAAAGCCCAAAGGTGATGCTACAGTGTCCTATGAAGACCAACCAACTGCCAAGGCTGCCGTGGAGTGGTTTG
ATGGGAAAGATTTCCAAGGGAGCAAGCTTAAGGTGTCTTTTGCTCGGAAGAAGCCTCCGATGAACAGCATGCGGGGTGCT
ATGCCTCCCCGTGAGGGCAGAAGGATGCTGCCGCCGCTCCGTGGAGGTCCCAGGGGCCCAGGATGTCCTGGGGGCCCCAT
GGGTCACATGGGAGGCTGTGGAGGAGACAGAGGTGGCTTTCGCCCAAGAGGGCCCCGGGGTTCTCGAGGGAACCCATCCG
GAGGAGGAAACTTCCTGCACCGAGCTGGAGACTGGCAGTGCCCCAATCCGGGGTGTGGAAACCAGAACTTCGCCTGGAGA
ACAGAATGCAACTGGTGCAAGGCCCCGAAGCCTGAAGGCTTCCTTCCACCACCCTTTCCACCCCTGGGTGGTGACCGTGG
CAGAGGCGGCCCTGGTGGCATGCGGGGCGGAAGAGGCGGCCTCATGGACCGCGGTGGTCCTGGTGGCGTGTTCAGAGGTG
GAAGTGGTGGAGACAGAGGGGGCTTCCATGATGGCCGGGCATAGACCAAGGTGGCTTTGGTGGAGGAAGACGGGGCGGCC
CTGGTGGGCCCCCTGCACCTTTGATGGAACAGATGGGAGGAAGAAGAGGCGGACGCGTAGGACCTGGAAAAATGGAAAAA
GATCAGCACCGTCAGGAACTCAGAGACCAGCCC

Alignment

ORF - retro_amel_191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.43 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLDYSTYSQAAAQQGYSAYTAQPTQGYAQTTQQAYGQKSYGTYGQPTDVSYTQAQTTATYGQTAYATSYG
          S.DYSTYSQAAAQ.GYSA.T.QPTQGYAQTTQ.AY.Q.SYGTYGQPTDVSYTQAQTTATYGQTAYATSYG
Retrocopy STDYSTYSQAAAQPGYSAHTTQPTQGYAQTTQ-AYAQQSYGTYGQPTDVSYTQAQTTATYGQTAYATSYG

Parental  QPPAGYTTPTAPQAYSQPVQGYGTGAYDTTTATVTTTQVSYAAQSACGTQPVYPAYGQQPAATAPARPQD
          QPPAGYTTPTA.QA.SQ.VQGYGTGAYDTTTAT.TTTQ.SYAAQSA.GTQP.Y.AYG..PAATAP.RPQD
Retrocopy QPPAGYTTPTATQA*SQHVQGYGTGAYDTTTATATTTQASYAAQSAYGTQPAYSAYGKEPAATAPERPQD

Parental  GNKPAETSQPQSSTGGYNQPSLGYGQSNYSYPQVPGSYPMQPVTAPPSYPPTSYSSTQPTSYDQSSYSQQ
          GNKPAETSQPQSSTGGYNQPSLGYGQSNYSYPQVPGSYPMQ.VTAPPSY.PTSYSSTQ.TSYDQSSYSQQ
Retrocopy GNKPAETSQPQSSTGGYNQPSLGYGQSNYSYPQVPGSYPMQLVTAPPSYSPTSYSSTQTTSYDQSSYSQQ

Parental  NTYGQP-SSYGQQSSYGQQSSYGQQPPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQ
          NTYGQP..SYGQQSSYGQ.SSYG.QPPTSYPP.TGSYSQAPSQYSQQSSSYGQQSSF.QDHPSSMGVYGQ
Retrocopy NTYGQP<ESYGQQSSYGQKSSYGHQPPTSYPP*TGSYSQAPSQYSQQSSSYGQQSSFQQDHPSSMGVYGQ

Parental  ESGGFSGPGENRS-MSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMGSAGERGGFNKPGGPMDEGPDLDLG
          .SGGFS.PGENR..MSGPDN.GRG.GGF..GGMSRGG.GGG.GGMG.AGERG.FNKPGGP.DEGPDLDLG
Retrocopy DSGGFSRPGENRA<MSGPDNGGRGSGGFGSGGMSRGGQGGGHGGMG-AGERGVFNKPGGPTDEGPDLDLG

Parental  PPVDPDEDCDNSAIYVQGLNDSVTLDDLADFFKQCGVVRMNKRTGQPMIHIYLDKETGKPKGDATVSYED
          ..VD.DED.DNSA..VQG.NDS.TLDDLADF.KQCGVV.MNKRTGQPMIHIYLDKETGKPKGDATVSYED
Retrocopy LRVDRDEDSDNSAVHVQG*NDSGTLDDLADFLKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED

Parental  PPTAKAAVEWFDGKDFQGSKLKVSFARKKPPMNSMRGAMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGG
          .PTAKAAVEWFDGKDFQGSKLKVSFARKKPPMNSMRGAMPPREGR.M.PPLRGGP.GPG.PGGPMG.MGG
Retrocopy QPTAKAAVEWFDGKDFQGSKLKVSFARKKPPMNSMRGAMPPREGRRMLPPLRGGPRGPGCPGGPMGHMGG

Parental  RGGDRGGFPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPP
          .GGDRGGF.PRGPRGSRGNPSGGGN..HRAGDWQCPNPGCGNQNFAWRTECN.CKAPKPEGFLPPPFPP.
Retrocopy CGGDRGGFRPRGPRGSRGNPSGGGNFLHRAGDWQCPNPGCGNQNFAWRTECNWCKAPKPEGFLPPPFPPL

Parental  GGDRGRGGPGGMRGGRGGLMDRGGPGGMFRGGRGGDRGGFRGGR-GMDRGGFGGGRRGGPGGPPGPLMEQ
          GGDRGRGGPGGMRGGRGGLMDRGGPGG.FRGG.GGDRGGF..GR.G.D.GGFGGGRRGGPGGPP.PLMEQ
Retrocopy GGDRGRGGPGGMRGGRGGLMDRGGPGGVFRGGSGGDRGGFHDGR<GIDQGGFGGGRRGGPGGPPAPLMEQ

Parental  MGGRRGGRGGPGKMDKGEHRQERRDRP
          MGGRRGGR.GPGKM.K..HRQE.RD.P
Retrocopy MGGRRGGRVGPGKMEKDQHRQELRDQP

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_191 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_191 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 14 parental genes, and 26 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,
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,