RetrogeneDB ID: retro_amel_1404

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193329.1:445108..445778(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSAMEG00000017075
• Aliases: None
• Description: programmed cell death 2 [Source:HGNC Symbol;Acc:8762]

Sequence

>retro_amel_1404
TTTAGAAATCAGCTACTTAGGAAAAACAATATTTACTCCTGTGACCATCTTCTGAGCATCCCCTTCCAGAGACAGGGTCG
TCTCTGTGCCTTTAGCTCAGGTCTAATGCTCATCTCTGGGGGTTTGTGGATGTTTAGGCCCCAAAGCATGCTCCAGATGT
CACATGGCCCGTCACTGCGGCAAAGAGCATCAGACTCTAGACGGGAGATCTGAGCATAAGCCTGTTTATACACAGCTATA
TTATTTGGACAGAACAATTCCAGACCACAACTTCCTTTAACCAAAATTTGAAACTGTAGCAGAAACAGAAGATGAGACTA
CACCTGAAGTTGTTGAAAAAGAAAATGAATCAGAAATTATGGGGAGCCCGGGTGAAGCACCTGAGGGAGAATTGGATTCC
ATGGCAAAACATGAATCCAAGGAAGATAAAATTTTCCAGAACTTTAAAACTAAAATAGCCCTTGAGCCAGAGCAGGTTCT
CAGATACGGCAAAGGGACTGCACCCATCTGGATCTCTGGTGAAAATAACCCTCAAGGAAAGGCTATTCCATATTGCCCCC
GTGGTGCCAAGACAATATTTGAATTCCAGGTCAGGCCTCAGCTTCTCAACTCCCTAAAGGCTGACAGGCTGGGCAGGAGT
GTCGATTGTGTTGTCCTGGCTGTCTTCACC

Alignment

ORF - retro_amel_1404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.22 %
• Parental protein coverage: 67.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FRNQLPRKNDFYSYE-PPSEDPPPETGESVCLQLKAGAHL-CRVCGCLGPKTCSRCHKAHYCSKEHQTLD
          FRNQL.RKN..YS...P.SE.P.PETG.S.CL.L...AHL...VCGCLGPK.CSRCH.A..C.KEHQTLD
Retrocopy FRNQLLRKNNIYSCD<PSSEHPLPETGSSLCL*LRSNAHL<LGVCGCLGPKACSRCHMARHCGKEHQTLD

Parental  WRFGHKQACTQSDYLERTIPDHNFLFPEFEIVIETEDEITPEVVEKENESEIMGSMGEAPEEELDSMAKH
          .R..HK...TQ..YL.RTIPDHNFL.P.FE.V.ETEDE.TPEVVEKENESEIMGS.GEAPE.ELDSMAKH
Retrocopy GRSEHKPVYTQLYYLDRTIPDHNFL*PKFETVAETEDETTPEVVEKENESEIMGSPGEAPEGELDSMAKH

Parental  ESREDKIFQKFKTKVALEPEQVLRYGRGITPIWISGENIPQEEDIPHCPCGAKRIFEFQVMPQLLNHLKA
          ES.EDKIFQ.FKTK.ALEPEQVLRYG.G..PIWISGEN.PQ...IP.CP.GAK.IFEFQV.PQLLN.LKA
Retrocopy ESKEDKIFQNFKTKIALEPEQVLRYGKGTAPIWISGENNPQGKAIPYCPRGAKTIFEFQVRPQLLNSLKA

Parental  DRLGRSVDWGVLAVFT
          DRLGRSVD..VLAVFT
Retrocopy DRLGRSVDCVVLAVFT

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_1404 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1404 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017075	2 retrocopies	retro_amel_1329, retro_amel_1404 ,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,