RetrogeneDB ID: retro_amel_1628

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193796.1:407872..408380(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCUR1
• Ensembl ID: ENSAMEG00000000395
• Aliases: None
• Description: mitochondrial calcium uniporter regulator 1 [Source:HGNC Symbol;Acc:21097]

Sequence

>retro_amel_1628
ACTATATATACATTCGTCAAGACCATGGAGGCCATCAGGAATATCACTTCAAAGGTTGGTTACCAACATGAAGCCGAGAT
CACTCTTCAGCAAATAATGTCTTGGGGTGCTAATGTGGAAAAGGGAGTAGTTGTTTTGGGGAAGAATGAACTTTCATCTT
CAGAGCGGAAAGTGAGAAAATAAAATGGGAACTGCATCTGTTAAAAGAATTAGTGGATGAAGTAATAAAAATCTGAACAG
AGAGTAAGTTTGATTTCAACTTAGAAAGAAGCAGAGTAAAAGAATTGTGTTCATTGAATGAAAGGAAGCTTCTGGAAGTG
AAGACAGACATGGTGGTATTTCATGCCAAGCAAGATCCCACCCTCATCCAGACAGACAGGAAGATAGACTCTGTGGTTGC
CAGCCTCAAAACCACACTCCAGTCACACAAGCCTGGTAATATTAAATATTTAGCGGGTCTGTATTTACCTGCATATTGGT
GGCTCTGGGATTTTATCGCCTGTGGATA

Alignment

ORF - retro_amel_1628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.34 %
• Parental protein coverage: 73.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TVSALVKITDANMDIVYKDMVTKMQQEITVQQIMSQIANVKKDMIILEKSEFSA-LRAENEKINVELHRL
          T....VK...A...I..K........EIT.QQIMS..ANV.K....L.K.E.S...RAE.EKI..ELH.L
Retrocopy TIYTFVKTMEAIRNITSK-VGYQHEAEITLQQIMSWGANVEKGVVVLGKNELSS<FRAESEKIKWELHLL

Parental  KQQVMDEVVKVRTDTKLDFNLEKSRVKELYSLNERKLLEMRTEMVALHAQQDRAVTQTDRKIDTEVAGLK
          K..V.DEV.K..T..K.DFNLE.SRVKEL.SLNERKLLE..T.MV..HA.QD....QTDRKID..VA.LK
Retrocopy KELV-DEVIKI*TESKFDFNLERSRVKELCSLNERKLLEVKTDMVVFHAKQDPTLIQTDRKIDSVVASLK

Parental  TMLESHKLDNIKYLA-GSVFTCLTVALGFYRLWI
          T.L.SHK..NIKYLA.GSVFTC..VALGFYRLWI
Retrocopy TTLQSHKPGNIKYLA<GSVFTCILVALGFYRLWI

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_1628 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1628 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000395	2 retrocopies	retro_amel_1628 , retro_amel_473,
Canis familiaris	ENSCAFG00000009857	3 retrocopies	retro_cfam_1018, retro_cfam_1556, retro_cfam_823,
Callithrix jacchus	ENSCJAG00000016050	1 retrocopy	retro_cjac_2522,
Cavia porcellus	ENSCPOG00000014899	1 retrocopy	retro_cpor_934,
Equus caballus	ENSECAG00000009150	2 retrocopies	retro_ecab_273, retro_ecab_469,
Felis catus	ENSFCAG00000005972	3 retrocopies	retro_fcat_1290, retro_fcat_1405, retro_fcat_1538,
Homo sapiens	ENSG00000050393	1 retrocopy	retro_hsap_1795,
Gorilla gorilla	ENSGGOG00000002632	1 retrocopy	retro_ggor_1320,
Loxodonta africana	ENSLAFG00000003287	2 retrocopies	retro_lafr_1252, retro_lafr_870,
Microcebus murinus	ENSMICG00000000183	2 retrocopies	retro_mmur_280, retro_mmur_580,
Myotis lucifugus	ENSMLUG00000010975	1 retrocopy	retro_mluc_1574,
Mustela putorius furo	ENSMPUG00000000698	1 retrocopy	retro_mputfur_640,
Nomascus leucogenys	ENSNLEG00000000914	1 retrocopy	retro_nleu_2768,
Otolemur garnettii	ENSOGAG00000013458	3 retrocopies	retro_ogar_1587, retro_ogar_1819, retro_ogar_3178,
Pan troglodytes	ENSPTRG00000017740	1 retrocopy	retro_ptro_1200,
Tarsius syrichta	ENSTSYG00000012562	1 retrocopy	retro_tsyr_810,
Tursiops truncatus	ENSTTRG00000012874	1 retrocopy	retro_ttru_1597,