RetrogeneDB ID: retro_amel_255

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192366.1:1931678..1932464(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000013407
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A6
• Ensembl ID: ENSAMEG00000005609
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6 [Source:HGNC Symbol;Acc:10992]

Sequence

>retro_amel_255
GTGGGTAAGCTGCTGCTGCAGGTGCAGCCTGCCAGCGAGCAAAGCACCACGGATAAGCAATACAAGGGCATTACATACAA
GTGTGGTTTGTATCCCTATAGAGCAGCGATTCCTGTCCTTCTGCCTGATAACCTGGCCAATGTCAACAGATACTTCCCTG
CTCAGGCTCTCAACCTGGCCTTCAAAGATAAATACAAGCAGATCTTCCTGGGTGGTGTGGACAAGGGAACCCGGTTTTGG
TGCTACTTTGCAGGGAATCTGGCATCCAGTGGTGCCACTGGGGCCACATCCTTGTGTTTTGTGTATCCTCTTGATTTTGT
GCTTAACAGGCTAGCCATGGGTGTGGGCAAAGCTGGAGCGGAAAGGGAATTCAGAGGCCTCTTGACTGTCTGGTTAAGAT
TACAAATCTGGTGGAATTAAGGGCCTAAATCAAGTTTAATGTGTCTGTGCAGGGTATGCTCATCCACCGAGCTGCCTACT
TCCGCAACGAGGACACTGCACAGGGAATGCTTCCAATCCCAAGGATACCACCAACTTCATCAGCTGAATGATCGCACAGT
CTGTCACGGTGGTTGCTGGGTTGACTTCCTCTCCGTTTGACACTGTTTGTGGCCGTACAACGGTGCACTCAGGGCACAAA
GGAACTGACATGTATAAGGCACGCTTGCCTGCTGGAGGAAGATTGCTCGTGATGAAGGAGCCAAAGCTTGTTTCAAGGGA
GCAAGGATCAAAGTTATTAGAGGCATGGGTGGTGCTTTTGTGCTTGTCTTATATGATGAAATCAAG

Alignment

ORF - retro_amel_255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.3 %
• Parental protein coverage: 92.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VRRSVLQVQHASKQIAADKQYKGIV-DCIVRIPKEQGVLSFWR-GNLANVIRYFPTQALNFAFKDKYKQI
          V....LQVQ.AS.Q...DKQYKGI.....V.IP.EQ..LSF....NLANV.RYFP.QALN.AFKDKYKQI
Retrocopy VGKLLLQVQPASEQSTTDKQYKGIT>TSVVCIPIEQRFLSFCL<DNLANVNRYFPAQALNLAFKDKYKQI

Parental  FLGGVDKHTQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKSGTEREFKGLG-DCLVKITKS
          FLGGVDK.T.FW.YFAGNLAS.GA.GATSLCFVYPLDF...RLA..VGK.G.EREF.GL..DCLVKIT..
Retrocopy FLGGVDKGTRFWCYFAGNLASSGATGATSLCFVYPLDFVLNRLAMGVGKAGAEREFRGLL<DCLVKITNL

Parental  DGIRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLP-DPKNTHIVVSWMIAQTVTAVAGVVSYPFDTVRR
          ...R.....FNVSVQG..I.RAAYF...DTA.GMLP..PK.T....S.MIAQ.VT.VAG..S.PFDTV..
Retrocopy VELRA*IK-FNVSVQGMLIHRAAYFRNEDTAQGMLP<NPKDTTNFIS*MIAQSVTVVAGLTSSPFDTVCG

Parental  RMMMQSGRKGADIMYK-GTVDCWRKILKDEGGKAFFKGAWSNVLRGMGGAFVLVLYDELK
          R....SG.KG.D.MYK.GT..CWRKI..DEG.KA.FKGA...V.RGMGGAFVLVLYDE.K
Retrocopy RTTVHSGHKGTD-MYK<GTLACWRKIARDEGAKACFKGARIKVIRGMGGAFVLVLYDEIK

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_255 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_255 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000143	1 retrocopy	retro_amel_1291,
Ailuropoda melanoleuca	ENSAMEG00000005609	1 retrocopy	retro_amel_255 ,
Homo sapiens	ENSG00000169100	5 retrocopies	retro_hsap_1207, retro_hsap_150, retro_hsap_2460, retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla	ENSGGOG00000023004	2 retrocopies	retro_ggor_239, retro_ggor_2785,
Loxodonta africana	ENSLAFG00000001584	1 retrocopy	retro_lafr_713,
Microcebus murinus	ENSMICG00000006136	2 retrocopies	retro_mmur_1021, retro_mmur_922,
Macaca mulatta	ENSMMUG00000006899	1 retrocopy	retro_mmul_1182,
Nomascus leucogenys	ENSNLEG00000000389	1 retrocopy	retro_nleu_895,
Otolemur garnettii	ENSOGAG00000000963	2 retrocopies	retro_ogar_2492, retro_ogar_2499,