RetrogeneDB ID: retro_amel_532

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192489.1:1907681..1908239(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HENMT1
• Ensembl ID: ENSAMEG00000004357
• Aliases: None
• Description: None

Sequence

>retro_amel_532
AAATTGACTCCAACAGCTGGGGATTATCTAGCTCCTTGGGACCTAGGTTTGACTGTAACTTTGTATCATGGTTTTGCTGT
ACAGAAAGACTCTCATTTGCTTGGATTTGACTTGATAACATGTATTGAATTGATGGAACACTTAGATTCTGAAGATCTGG
TCAAGTTTCTTGAAGCTGTATTTGGGTACTTTTCTCCAGGTATGGTTGTCATCAGCACACCAAACTCTGCATTCAATCTC
TGTTTCCAACATCAACCTTTAGGAAGCCAGATCACAAATTTGAGTGGAACAGAATACAGTTTCAGATGTGGGCTTTGGAT
GTAGCAAATCTCTACAATTACTCCATTGAGTTTACTGGTGTGGGGGCTCCACCAACAGGAGCTGAGCATGTTGGTACTGT
ACGTAGATAGGGGCTTACAGAAAAACATAGCAAAGGCAACAGAATTGTGCATTTCAGAGCCACAGGAACATGTTTATAAA
GCTGTTTTAACAACTTCATAACCGAGACAGTAAAAAGTATACCTCCAGCTTGTTCTGAGTGCCGAGGTGTTAAAAAGC

Alignment

ORF - retro_amel_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 50.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RLSPGVGGFIIPRELDLTITLYRGSAVQKDSRLRGFDLITCIELIEHLDSEDLAKFPEVVFGYFSPGMVV
          .L.P..G....P..L.LT.TLY.G.AVQKDS.L.GFDLITCIEL.EHLDSEDL.KF.E.VFGYFSPGMVV
Retrocopy KLTPTAGDYLAPWDLGLTVTLYHGFAVQKDSHLLGFDLITCIELMEHLDSEDLVKFLEAVFGYFSPGMVV

Parental  ISTPNSEFN-PLFPASTFRNPDHRFEWDRKQFQTWALDVGKLYSYSVEFTGVGDPPAGAEHVG-YCTQIG
          ISTPNS.FN..LFP.STFR.PDH.FEW.R.QFQ.WALDV..LY.YS.EFTGVG.PP.GAEHVG.YCT.IG
Retrocopy ISTPNSAFN<SLFPTSTFRKPDHKFEWNRIQFQMWALDVANLYNYSIEFTGVGAPPTGAEHVG<YCT*IG

Parental  VF-QKNIAKATGSSISEPEEHVYEVVYRTSYPSLQQRKYFRFTLSIEVVKA
          ...QKNIAKAT...ISEP.EHVY..V..TS.P..Q...Y....LS.EV.K.
Retrocopy AY<QKNIAKATELCISEPQEHVYKAVLTTS*PR-Q*KVYLQLVLSAEVLKS

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_532 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_532 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004357	1 retrocopy	retro_amel_532 ,
Otolemur garnettii	ENSOGAG00000013441	4 retrocopies	retro_ogar_1961, retro_ogar_2013, retro_ogar_2135, retro_ogar_562,
Sus scrofa	ENSSSCG00000006846	1 retrocopy	retro_sscr_80,