RetrogeneDB ID: retro_amel_719

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192587.1:1084889..1085338(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSAMEG00000015041
• Aliases: None
• Description: thioredoxin-related transmembrane protein 1 [Source:HGNC Symbol;Acc:15487]

Sequence

>retro_amel_719
ATGGTTCCCATGACAGTGCTGCTCCTATTGCTTTGTGGGGCTCCCTGGACCAATGGGCACCAGAGTGATGTGCCCATCAT
CATGGTAAGAACCCAAAAGAGTTGCTGGAATGAGAATAGTCGATAGAACTTTATGCCCCATGGTATCCTACTTGTTAGAA
TCTTCAACCAGAATGGGAAAGTGTTACTGAATGGAGAGAAGATCTTGAGGTTAATGTTGCAAAAGTATATGTCACAGAGC
AGCCAAGGCTGAGTGGATGATTTATCACAATTGCTCTTCCTACTATTTATCATTGTAAAGATGGTGAATTTAGGTGCTAT
CAGAGCTCACGGAATAAGAAGGACTTCATAAACTTTATAAATGAGCAAGAGTGTAAGAGTATTGAACCCATTTCATCATG
GTTTGGTCCAGGTTCTGTTCTGTATGTCAGCACTCTTTCAACTATCTAT

Alignment

ORF - retro_amel_719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 53.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVPVAVLLLLLWGAPWTHGRRSDVRVIT-DENWKELLEGEWMIEFYAPWCPACQNLQPEWESFAEWGEDL
          .VP..VLLLLL.GAPWT.G..SDV..I....N.KELLE.E..IE.YAPW.P.C.NLQPEWES..EW.EDL
Retrocopy MVPMTVLLLLLCGAPWTNGHQSDVPIIM<GKNPKELLE*E*SIELYAPWYPTC*NLQPEWESVTEWREDL

Parental  EVNVAKVDVTEQPGLSGRFIITALPTIYHCKGGEFRRYQGPRTKKDFINFISEKEWKSIEPVSSWFGPGS
          EVNVAKV.VTEQP.LSG.FI..ALPTIYHCK.GEFR.YQ..R.KKDFINFI.E.E.KSIEP.SSWFGPGS
Retrocopy EVNVAKVYVTEQPRLSG*FITIALPTIYHCKDGEFRCYQSSRNKKDFINFINEQECKSIEPISSWFGPGS

Parental  VL-MSSMSALF
          VL..S..S...
Retrocopy VLYVSTLSTIY

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_719 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_719 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015041	1 retrocopy	retro_amel_719 ,
Canis familiaris	ENSCAFG00000014626	1 retrocopy	retro_cfam_796,
Choloepus hoffmanni	ENSCHOG00000011305	1 retrocopy	retro_chof_1249,
Callithrix jacchus	ENSCJAG00000006893	1 retrocopy	retro_cjac_1453,
Dasypus novemcinctus	ENSDNOG00000016496	1 retrocopy	retro_dnov_78,
Felis catus	ENSFCAG00000002780	1 retrocopy	retro_fcat_333,
Homo sapiens	ENSG00000139921	2 retrocopies	retro_hsap_3840, retro_hsap_3970,
Gorilla gorilla	ENSGGOG00000009768	1 retrocopy	retro_ggor_2587,
Loxodonta africana	ENSLAFG00000013251	1 retrocopy	retro_lafr_1214,
Macaca mulatta	ENSMMUG00000001901	1 retrocopy	retro_mmul_1618,
Nomascus leucogenys	ENSNLEG00000012362	2 retrocopies	retro_nleu_1976, retro_nleu_2524,
Oryctolagus cuniculus	ENSOCUG00000003980	1 retrocopy	retro_ocun_571,
Pongo abelii	ENSPPYG00000005810	2 retrocopies	retro_pabe_3058, retro_pabe_3264,
Pan troglodytes	ENSPTRG00000006339	2 retrocopies	retro_ptro_2522, retro_ptro_2695,