RetrogeneDB ID: retro_amel_377

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192411.1:2588198..2588639(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5S
• Ensembl ID: ENSAMEG00000009828
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit s (factor B) [Source:HGNC Symbol;Acc:18799]

Sequence

>retro_amel_377
TGGCCACCGCGCCCTGGGGCCCTGGTGCACCACCCCGGCCCGGAGAGGTGGAGCGGGACTACCACAACCCCCCCACACAG
GCCCTCTGGGCAAATACAAGATTCAGGCAATTGATGCCACCAACTCCTGTATCACCAGCGTTGTCTCTGGTCACAGGAGC
ACTTACAGCATGTTGGAAAAATAAGGCTATGAGCGTGTCATTAAATCAAGGCCCAGTGCTTGGAGAGACTTGGTAAACTT
AAAAATGTATGAAAAAGCTTGCTGGAAATGGAAACAATTTCATGTGGGAATATCGCAGACAAGGACATCATTGCTTTACA
TCGCTTAAGAAACCTCAAGTATTTGTTGTTAAGTGATCTTCCTGGAATGAGAGAAAAAGAAAACCTTCTCCAAGCTTTTA
AGACAACACTGCCTTCTCTGGAACCGAAATTGGACTTGAAA

Alignment

ORF - retro_amel_377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66. %
• Parental protein coverage: 73.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WLLRCGAMVRYHGQEKWQKDYNHLP-TGPLDKYKIQAIDATDSCIMRIGFDHL-EGLQHVEKIRLCKCHY
          W..R.GA.V...G.E.W.......P.TGPL.KYKIQAIDAT.SCI......H..E.LQHV.KIRL..CH.
Retrocopy WPPRPGALVHHPGPERWSGTTTTPP>TGPLGKYKIQAIDATNSCITSVVSGHR<EHLQHVGKIRL*ACH*

Parental  IEDGCLERLGKLENLQKSILEMEIISCGNITDKGIIALYHLSRNLKYLLLSDLPGVREKENLIRTFKTVL
          I...CLERLGKL.N..KS.LEME.ISCGNI.DK.IIAL..L.RNLKYLLLSDLPG.REKENL...FKT.L
Retrocopy IKAQCLERLGKLKNV*KSLLEMETISCGNIADKDIIALHRL-RNLKYLLLSDLPGMREKENLLQAFKTTL

Parental  PSLELKLDLK
          PSLE.KLDLK
Retrocopy PSLEPKLDLK

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_377 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_377 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009828	1 retrocopy	retro_amel_377 ,
Canis familiaris	ENSCAFG00000014285	1 retrocopy	retro_cfam_267,
Cavia porcellus	ENSCPOG00000014471	1 retrocopy	retro_cpor_740,
Felis catus	ENSFCAG00000029962	1 retrocopy	retro_fcat_72,
Loxodonta africana	ENSLAFG00000013773	1 retrocopy	retro_lafr_167,
Pteropus vampyrus	ENSPVAG00000006173	1 retrocopy	retro_pvam_539,
Sorex araneus	ENSSARG00000007707	1 retrocopy	retro_sara_694,