RetrogeneDB ID: retro_amel_959

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192769.1:1091182..1092547(+)
• Located in intron of: None

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_959
CCAACTAGTTATGATTAGAGTAGTTACTCTCAGCAGAACACCTATGGGCAGCCCAGCAGCTATGGAGAGCAGAGTAGCTA
TGGTCAACACAGCAGCTATGGACAGCAGCCACCCACTAGTTATCCCCCACAAACTGGATCCTACAGCCAGGCTCCAAGTC
CATATAGCCAGCAGAGCAGCAGCTATGGTCAGCAGAGTTCATTCTGACAGGACCACCCCAGTAGCATGAGTATTTATGGA
CAGGAGTCTGGAGGATTTTCCAGACCAGGAGAGAATGGGAATGTGAGTGGGCCTGATAACCGGGGCAGGGGAAGAGGGGG
ATTTGATTGTGGAGGCATGTGCAGAGGTGGACAGGGAGGAGAACACAGTGGAATGGGTGCTGGAGAGCGAGGTGGCTTCA
GTAAGCCTGACAGATCCATGGTTGAAGGACCAGATATTGATCTAGGTCCACCTGTAGATCCAGATGAAGACTCTGACAAC
AGTGCAGTTTATGTGCAAGGCTGAAATGACAGTGTGATCCTAGATGATCTGGCAGACTTCGTTAAGCAGTGTGGAGTTGT
TAAGATAAACAAGAGAACTGGATAACCCATGATTCATGTCTACTTGGACAAGGAAACAGGAAAGCCCAAAGGTGTTGCTA
CAGTGTCCTATGAAGACCCACCAACTGCCAAGGTTGCCATGGAGTGGTTTGATGGTAAAGATTTTCAAGGGAGCAAATTT
AAGGTTTCTCTTGCCAGAAGAAGCCTCTGATGAACAGCATGCAGGGTGGTATGCCTCCCTGTGAGGGCAGAGGGATGCTG
CAGCCACTCTGTGGAGGTCCAGGGGGCCCAGGAGGTCCTGGGGGTCCCATGGGTCACAGAAGAGGCCGTGGAGGAGACAG
AGGTAGCTTTCCCCCAAGAGGGCCCCGGGATTCCTGAGGGAACCCACCCAGAGGAGGAAAACGTCCAGCACTGAGCTGGA
GACTGGCAGTGCCCCAGTCTGGGTTGTGGAAACCAGAACTAGGCCTGGAGAGCAGAATGCAAGCAGTGTGAGGCCTTGAA
GCCTGAAGGCTTCCTTCCATCACCCTTTCTACACCCTGGGCAGTGACCATGGCAGAGGTGGCCCCGGTGGCATGCGGGGT
GGAAGAGGCAGCCTCATGGACCATGGTGGTCCCGGTGGGATGTTCAGAAGTGGTCATGGTGGAGAAAGAGGTGGCTTCCA
TGGTGGCCAGGGCATGGACTGAGGTGGCTTTGGTGGAGGAAGAGGGGCGGCCCTGGTGGGCCCCCTGGACCTTTGATGGA
ACAGATGGGAGGAAGAAGAGGTGGGCATGGAGGACCGGGAAAAATGGAAAAAGATCAGCACCGTCAGGAACTCAGAGACC
AGCCC

Alignment

ORF - retro_amel_959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.92 %
• Parental protein coverage: 68.84 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PTSYDQSSYSQQNTYGQPSSYGQQSSYGQQSSYGQQPPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQ
          PTSYD.SSYSQQNTYGQPSSYG.QSSYGQ.SSYGQQPPTSYPPQTGSYSQAPS.YSQQSSSYGQQSSF.Q
Retrocopy PTSYD*SSYSQQNTYGQPSSYGEQSSYGQHSSYGQQPPTSYPPQTGSYSQAPSPYSQQSSSYGQQSSF*Q

Parental  DHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMGAGERGGFNKPGGPM
          DHPSSM..YGQESGGFS.PGEN...SGPDNRGRGRGGFD.GGM.RGG.GG...GMGAGERGGF.KP...M
Retrocopy DHPSSMSIYGQESGGFSRPGENGNVSGPDNRGRGRGGFDCGGMCRGGQGGEHSGMGAGERGGFSKPDRSM

Parental  DEGPDLDLGPPVDPDEDCDNSAIYVQGLNDSVTLDDLADFFKQCGVVRMNKRTGQPMIHIYLDKETGKPK
          .EGPD.DLGPPVDPDED.DNSA.YVQG.NDSV.LDDLADF.KQCGVV..NKRTG.PMIH.YLDKETGKPK
Retrocopy VEGPDIDLGPPVDPDEDSDNSAVYVQG*NDSVILDDLADFVKQCGVVKINKRTG*PMIHVYLDKETGKPK

Parental  GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSFAR-KKPPMNSMRGAMPPREGRGMPPPLRGGPGGPGG
          G.ATVSYEDPPTAK.A.EWFDGKDFQGSK.KVS.AR.KKP.MNSM.G.MPP.EGRGM..PL.GGPGGPGG
Retrocopy GVATVSYEDPPTAKVAMEWFDGKDFQGSKFKVSLAR<KKPLMNSMQGGMPPCEGRGMLQPLCGGPGGPGG

Parental  PGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGG-NVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKP
          PGGPMG...GRGGDRG.FPPRGPR.S.GNP..GG.NVQH.AGDWQCP..GCGNQN.AWR.EC.QC.A.KP
Retrocopy PGGPMGHRRGRGGDRGSFPPRGPRDS*GNPPRGG>NVQH*AGDWQCPSLGCGNQN*AWRAECKQCEALKP

Parental  EGFLPPPFPPP-GGDRGRGGPGGMRGGRGGLMDRGGPGGMFRGGRGGDRGGFRGGRGMDRGGFGGGR-RG
          EGFLP.PF..P.G.D.GRGGPGGMRGGRG.LMD.GGPGGMFR.G.GG.RGGF.GG.GMD.GGFGGGR.RG
Retrocopy EGFLPSPFLHP>GSDHGRGGPGGMRGGRGSLMDHGGPGGMFRSGHGGERGGFHGGQGMD*GGFGGGR<RG

Parental  GPGGPPGPLMEQMGGRRGGRGGPGKMDKGEHRQERRDRP
          GPGGPPGPLMEQMGGRRGG.GGPGKM.K..HRQE.RD.P
Retrocopy GPGGPPGPLMEQMGGRRGGHGGPGKMEKDQHRQELRDQP

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_959 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_959 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,