RetrogeneDB ID: retro_amel_862

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192689.1:43394..43941(+)
• Located in intron of: ENSAMEG00000015209

Retrocopy information

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

Parental gene information

• Parental gene symbol: HESX1
• Ensembl ID: ENSAMEG00000011722
• Aliases: None
• Description: HESX homeobox 1 [Source:HGNC Symbol;Acc:4877]

Sequence

>retro_amel_862
TCTCCCAACCTTCAGGAAGGTGCTTGGCTTGAGGAAAGCAAATCCTCACCCTGCTCCTTTTCAGCTGAGAGCATTTTAGG
ATTGGTCCAGAAGAAAAACTGTTCCATCAATGAAACCCCACAGGCCGTGCACAGACACCTGTGGCTCCTGAGGAAAAGAT
GTTAACCTATGTCTACATATCCTGAGCCTTCCTAATGGGATCTCATCCCCTTGTACGATGGATCACCCAGTGCCAGAAGA
AAGATTTCTGAAATATAAAAATTACTTTTCAGCCTCAGAAAGACTGTCTTCAAAAGAGAGCTGAGTCGGTATAGAGGCTG
AAGACCAAGAACTGCGTTTACTCAAAACCAGACTGAACTGCTGGAAAATGTCTTTAGAATAAACTGCTATCCCGGCATTG
ATATTGGAGAAGATAGCTCAAAAACTGAATCTAGAGCAAAAAATAATCTAGATCTGGTTCCAAAATCAGCATGCAAAGCT
GAAAACATCCCATAGAGAATCACTGTTTTTAATATTAAAAAAAAATTTCAACACATACCTCCTGGAA

Alignment

ORF - retro_amel_862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.78 %
• Parental protein coverage: 99.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APSLPEGARLGESK-PSPCSFSIESILGLDQKKDCVPSMKPHRPWADPCSSSGEDVNLCVHIPSLPNGIS
          .P.L.EGA.L.ESK.P.P..F...........K..VPSMKPHRP..D.C.S.G.DVNLC.HI.SLPNGIS
Retrocopy SPNLQEGAWLEESK>PHPAPFQLRAF*DWSRRKT-VPSMKPHRPCTDTCGS*GKDVNLCLHILSLPNGIS

Parental  FPCTVDRPMPEERFLKYENYFSASERLS-LKRELSWYRGRRPRTAFTQNQIEVLENVFRVNCY-PGIDIR
          .PCT.D.P.PEERFLKY.NYFSASERLS..KRELS.YRG.RPRTAFTQNQ.E.LENVFR.NCY.P...I.
Retrocopy SPCTMDHPVPEERFLKYKNYFSASERLS<FKRELSRYRG*RPRTAFTQNQTELLENVFRINCY>PAL-IL

Parental  EDLARKLNLEEDRIQIWFQNRRAKLKRSHRESQFLMAKKNFNTNLLE
          E..A.KLNLE...I.IWFQN..AKLK.SHRES.FL.....FNT.LLE
Retrocopy EKIAQKLNLEQKII*IWFQNQHAKLKTSHRESLFLIXXXXFNTYLLE

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_862 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_862 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011722	1 retrocopy	retro_amel_862 ,
Choloepus hoffmanni	ENSCHOG00000013897	1 retrocopy	retro_chof_123,
Callithrix jacchus	ENSCJAG00000010981	1 retrocopy	retro_cjac_891,
Cavia porcellus	ENSCPOG00000012741	1 retrocopy	retro_cpor_1067,
Dasypus novemcinctus	ENSDNOG00000003677	1 retrocopy	retro_dnov_58,
Mustela putorius furo	ENSMPUG00000016854	2 retrocopies	retro_mputfur_112, retro_mputfur_174,