RetrogeneDB ID: retro_amel_815

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192660.1:706245..706907(+)
• Located in intron of: ENSAMEG00000002169

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000017346
• Aliases: None
• Description: Aspartate aminotransferase [Source:UniProtKB/TrEMBL;Acc:G1MG53]

Sequence

>retro_amel_815
CTGCATGCTCCTGCCCACAATCCCATGGGAGTGGACCCTCATCCTGAGCAATAGAAGGCAACAGCAATAGCAGTGAAAAA
GAGAATCTCTCTACGTTCTTTGACATGGCCTACCAAGGCTTTGCCAATAGTAATGGTAACAAGGATGCCTGGGCTGTGCA
CCACTTCATCAAAGAGGGCATTAACGTTTGTCTCTGCCAATCCTATACCAAGAACACGGGCTTCTATGGTAAGTGTGTGG
GAGACTTCACTGTGCTCTGCAAAGATGCTGATGAAGTCAGAGGGGTAGAGTCACAATTGAAGACCTTGATCCATCTCATG
TATTCCAGCCCTCCTCTCAATGGAGCTCAGGTTGCCTTGACCATTCTGACCAGCCCTGATTTTCAAAAACAATAGTTGCA
GGAAGTACAAGTCATGGCCAACTGCATCATTAGTATCCGAATTCAGCTGGTCTTCAACCTCAAGAAGGAGGGCTTCTCCC
AACAATGGGCAGCATACCCCGACCAGGCTGGCATGTTCTGTTTCACAGGGCTAAAGCCTGAGCAGGTGGAGCAGCTGACC
GAGGAGTTCTCCATTTACATGAGAGAGGTCAGCCACATCTCTGTGGCAAGGGTCACTGGACAACTGGGCTACCTTGCTCA
TGACATTTACCAGGTCACCAAG

Alignment

ORF - retro_amel_815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.96 %
• Parental protein coverage: 51.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LHACAHNPTGVDPRPEQWKEMATVVKKN-NLFAFFDMAYQGFASGDGNKDAWAVRHFIEQGINVCLCQSY
          LHA.AHNP.GVDP.PEQ.K..A..VKK..NL..FFDMAYQGFA...GNKDAWAV.HFI..GINVCLCQSY
Retrocopy LHAPAHNPMGVDPHPEQ*KATAIAVKKR<NLSTFFDMAYQGFANSNGNKDAWAVHHFIKEGINVCLCQSY

Parental  AKNMGLYGERVGAFTVVCKDADEAKRVESQLKILIRPMYSNPPVNGARIASTILTSPDLRKQWLQEVKGM
          .KN.G.YG..VG.FTV.CKDADE...VESQLK.LI..MYS.PP.NGA..A.TILTSPD..KQ.LQEV..M
Retrocopy TKNTGFYGKCVGDFTVLCKDADEVRGVESQLKTLIHLMYSSPPLNGAQVALTILTSPDFQKQ*LQEVQVM

Parental  ADRIISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMTKDGRISVAGVTSGN
          A..IIS.R.QLV.NLKKEG.S..W....DQ.GMFCFTGLKPEQVE.LT.EFSIYM.....ISVA.VT.G.
Retrocopy ANCIISIRIQLVFNLKKEGFSQQWAAYPDQAGMFCFTGLKPEQVEQLTEEFSIYMREVSHISVARVT-GQ

Parental  VGYLAHAIHQVTK
          .GYLAH.I.QVTK
Retrocopy LGYLAHDIYQVTK

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_815 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_815 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 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815 , retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Equus caballus	ENSECAG00000016504	1 retrocopy	retro_ecab_694,
Felis catus	ENSFCAG00000025552	3 retrocopies	retro_fcat_1068, retro_fcat_1888, retro_fcat_381,
Homo sapiens	ENSG00000125166	4 retrocopies	retro_hsap_4687, retro_hsap_473, retro_hsap_960, retro_hsap_971,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macropus eugenii	ENSMEUG00000012574	1 retrocopy	retro_meug_2109,
Microcebus murinus	ENSMICG00000008954	1 retrocopy	retro_mmur_480,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Mus musculus	ENSMUSG00000031672	1 retrocopy	retro_mmus_2701,
Oryctolagus cuniculus	ENSOCUG00000003871	1 retrocopy	retro_ocun_1516,
Otolemur garnettii	ENSOGAG00000000551	2 retrocopies	retro_ogar_2182, retro_ogar_827,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Pan troglodytes	ENSPTRG00000008185	4 retrocopies	retro_ptro_3115, retro_ptro_354, retro_ptro_665, retro_ptro_670,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,
Tupaia belangeri	ENSTBEG00000001808	1 retrocopy	retro_tbel_3799,