RetrogeneDB ID: retro_amel_967

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192774.1:1157054..1157634(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YKT6
• Ensembl ID: ENSAMEG00000017618
• Aliases: None
• Description: YKT6 v-SNARE homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16959]

Sequence

>retro_amel_967
ATGAAGCTGTTAGGCCTCAGCGGACTGTACAAAGGCGAGCCCAAGGCCGTGCTGCTTAAAGCCATGGATGACATGTCCTC
GTTCAGCTTTTTCCAGAGGTCCAGTGCTCAGGACTTCATGACCTTCACAAGTCAACGGACTGTGGAGCCCTCAGCGGAAG
GCCGCAGAGCTTCTGTCAAAGAATGAGAATATCTGTGCCACCTCTACGTGTGAAACGACTGTCTTGCGGGGATGGTCGTA
ACGGACAGTGAATATCTGTCCTGGGGGGCTTTGCCTTGCCGGAGAAGATACTAGGTGAATTCTCCAAGCAGCTCGACAAG
ATAGAGTGGCCAGCCGATCCCCTGCTACCATCCACCACGTGGCCTTAGGTGACCACCTCAGAAGGTACCAGAACCTTGGA
GAAACTGGCCCCAAGCTCAAGGTGCTGTCTGAGCTGGATGTGACCCAAATCATTCTGCACAACACCATGGAGCGTCCGTT
AGAGCGAGGGGAGAAGCTAGATGACCTGGTGTCCAAACCCAAAGCGCTGCGAACACCGTCTAAAGCCCGGAAACGGCGCG
GAGACAGGACTTGTGCTGTG

Alignment

ORF - retro_amel_967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.33 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKLYSLSVLYKGDPKAVLLKAAYDVSSFSFFQRSSVQEFMTFTSQLIVERSAKGSRASVKEQEYLCHVYV
          MKL..LS.LYKG.PKAVLLKA..D.SSFSFFQRSS.Q.FMTFTSQ..VE.SA.G.RASVKE.EYLCH.YV
Retrocopy MKLLGLSGLYKGEPKAVLLKAMDDMSSFSFFQRSSAQDFMTFTSQRTVEPSAEGRRASVKE*EYLCHLYV

Parental  RNDSLAGVVIADSEYPSRVA-FSLLEKVLDEFSKQVDRIEWPVG-SPASIHYMALDGHLSRYQNPREADP
          .ND.LAG.V..DSEY.S..A.F.L.EK.L.EFSKQ.D.IEWP...SPA.IH..AL..HL.RYQN..E..P
Retrocopy *NDCLAGMVVTDSEYLSWGA<FALPEKILGEFSKQLDKIEWPAD<SPATIHHVALGDHLRRYQNLGETGP

Parental  MTKVQAELDETKIILHNTMESLLERGERLDDLVSKSEVLGTQSKAFYKTARKQNSCCAI
          ..KV..ELD.T.IILHNTME..LERGE.LDDLVSK...L.T.SKA.....R.....CA.
Retrocopy KLKVLSELDVTQIILHNTMERPLERGEKLDDLVSKPKALRTPSKA---RKRRGDRTCAV

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_967 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_967 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 20 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017618	1 retrocopy	retro_amel_967 ,
Bos taurus	ENSBTAG00000000274	1 retrocopy	retro_btau_601,
Canis familiaris	ENSCAFG00000002903	1 retrocopy	retro_cfam_740,
Choloepus hoffmanni	ENSCHOG00000011207	1 retrocopy	retro_chof_657,
Callithrix jacchus	ENSCJAG00000008053	2 retrocopies	retro_cjac_2394, retro_cjac_2492,
Dasypus novemcinctus	ENSDNOG00000015173	1 retrocopy	retro_dnov_1364,
Dipodomys ordii	ENSDORG00000016393	1 retrocopy	retro_dord_621,
Erinaceus europaeus	ENSEEUG00000001247	1 retrocopy	retro_eeur_267,
Felis catus	ENSFCAG00000014362	1 retrocopy	retro_fcat_1327,
Homo sapiens	ENSG00000106636	1 retrocopy	retro_hsap_3687,
Gorilla gorilla	ENSGGOG00000027036	1 retrocopy	retro_ggor_2493,
Macropus eugenii	ENSMEUG00000014769	1 retrocopy	retro_meug_2068,
Mustela putorius furo	ENSMPUG00000018200	2 retrocopies	retro_mputfur_141, retro_mputfur_165,
Mus musculus	ENSMUSG00000002741	1 retrocopy	retro_mmus_825,
Nomascus leucogenys	ENSNLEG00000003689	1 retrocopy	retro_nleu_2275,
Oryctolagus cuniculus	ENSOCUG00000002981	1 retrocopy	retro_ocun_15,
Pongo abelii	ENSPPYG00000017595	1 retrocopy	retro_pabe_3022,
Pan troglodytes	ENSPTRG00000019141	1 retrocopy	retro_ptro_2500,
Sus scrofa	ENSSSCG00000016750	1 retrocopy	retro_sscr_1063,
Tursiops truncatus	ENSTTRG00000006052	2 retrocopies	retro_ttru_1320, retro_ttru_417,