RetrogeneDB ID: retro_amel_612

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192527.1:148801..149759(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000016766
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDT9
• Ensembl ID: ENSAMEG00000003244
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 9 [Source:HGNC Symbol;Acc:8056]

Sequence

>retro_amel_612
GGCAGCTGCCCCATCATCTGAGCTGGTTGGAGCCTGTCTTCCTCACGTGCGGTTCCTCCAAGCTTCATCACGTCAGATTC
GAACGACGCCGCTGAGAACCCGCACAAGAAGGCCAGGACGTCTCCATACCCTGGCTCTAAAGTGGAGCGAAGCCAGGTCC
CCGATGAGAAAGTGAGCTGGCTGGTCCAGTGGCCAGATTACAAGCCTGTCGAGTACACTGCGGGTTCTGTCTTGGCCCAG
CCCTCGTGGGCAGATCCCCCGATGGGCGAAAGGAACTTCTCGCCTAAATTCAATGAGGAGGATGGGCATGTTGAAAGAAG
GAGCCAGAATGGTTTGTATGAGGTCGAGAGTGGCAGACCTAGAAATCCCACGGGTAGAACAGGGCTGGTGGGCAGAGGGC
TTTTAGGGCGGTGGGGTCCCAATCACGCTGCTGATCCCATCTTAACCAGGTGGAAAAACGATAGCAAGGGAAAGAAAGTG
ATCCATCCTGTTTCTGAGAGAAACGTCCTGCAATTTGTAGCCATCAAAAGGAAGGACTGTGGAGAATGGGCCCTCCCAGG
GGGAATGGTGGAGCCAGGAGAGAAAATTAGTACCACATTGAAGAGAGAATTTGGGGAGGAAGCCATGAATTCCTTACAGA
AATTTAGAGCAGAAACACAGGATTTGGAGAAACAACTGCACAAACTATTCAGTCAGGATACTTTGTGGTCTATAAAGTTA
CGTGGATGATCCCCGAAACACAGATAATGCGTGGATGGAAACTGAGGCTGTGAACTACCACGACGATACAGGTGAGATAA
TGGATCATCTTTCTCTGGAAGCTGGTGATGATGCCAAGAAAGTGAAATGGGTGGACATCAACGATCAACTCAAGCTTTAT
GCCAGCCATTCCCAATTTATTCAACTCGTGGCTGAGAAACGAGGTGACCATTGGAGGGAGGGCATGTCCTCCAACTGC

Alignment

ORF - retro_amel_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 91.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GCCSIPACRNTFSSCGFHLSSNIMSSSNGAKGNSHNKARTSPYPGSKVQRSQVPNEKVGWFVEWQDYNPV
          G.C.I.......SS......S.I.S.SN.A..N.H.KARTSPYPGSKV.RSQVP.EKV.W.V.W.DY.PV
Retrocopy GSCPII*AGWSLSSSRAVPPSFITSDSNDAAENPHKKARTSPYPGSKVERSQVPDEKVSWLVQWPDYKPV

Parental  EYTAVSVLAGPRWADPQISESNFSPKFNEKDGHVERKSQNGLYEIENGRPRNPAGRTGLIGRGLLGRWGP
          EYTA.SVLA.P.WADP...E.NFSPKFNE.DGHVER.SQNGLYE.E.GRPRNP.GRTGL.GRGLLGRWGP
Retrocopy EYTAGSVLAQPSWADPPMGERNFSPKFNEEDGHVERRSQNGLYEVESGRPRNPTGRTGLVGRGLLGRWGP

Parental  NHAADPIITRWKRDRSGNKVSHPISGKNILQFVAIRRKDCGEWAIPGGMVDPGEKISATLKREFGEEALN
          NHAADPI.TRWK.D..G.KV.HP.S..N.LQFVAI.RKDCGEWA.PGGMV.PGEKIS.TLKREFGEEA.N
Retrocopy NHAADPILTRWKNDSKGKKVIHPVSERNVLQFVAIKRKDCGEWALPGGMVEPGEKISTTLKREFGEEAMN

Parental  SLQKSGVEKRELEEQLHKLFSQE-HLVIYK-GYVDDPRNTDNAWMETEAVNYHDETVTGEIMDNLTLEAG
          SLQK...E...LE.QLHKLFSQ....V.YK..YVDDPRNTDNAWMETEAVNYHD...TGEIMD.L.LEAG
Retrocopy SLQKFRAETQDLEKQLHKLFSQD<YFVVYK<SYVDDPRNTDNAWMETEAVNYHDD--TGEIMDHLSLEAG

Parental  DDAGKVKWVDISDQLQLYASHSHFIKLVAEKRDAHWSEDSETEC
          DDA.KVKWVDI.DQL.LYASHS.FI.LVAEKR..HW.E.....C
Retrocopy DDAKKVKWVDINDQLKLYASHSQFIQLVAEKRGDHWREGMSSNC

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_612 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_612 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 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003244	1 retrocopy	retro_amel_612 ,
Bos taurus	ENSBTAG00000011354	1 retrocopy	retro_btau_1112,
Canis familiaris	ENSCAFG00000009529	1 retrocopy	retro_cfam_1271,
Callithrix jacchus	ENSCJAG00000006159	1 retrocopy	retro_cjac_1047,
Equus caballus	ENSECAG00000019556	1 retrocopy	retro_ecab_123,
Echinops telfairi	ENSETEG00000019164	1 retrocopy	retro_etel_348,
Felis catus	ENSFCAG00000003315	1 retrocopy	retro_fcat_1509,
Homo sapiens	ENSG00000170502	1 retrocopy	retro_hsap_709,
Gorilla gorilla	ENSGGOG00000014777	1 retrocopy	retro_ggor_602,
Loxodonta africana	ENSLAFG00000011391	1 retrocopy	retro_lafr_224,
Macropus eugenii	ENSMEUG00000012123	4 retrocopies	retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica	ENSMODG00000020738	2 retrocopies	retro_mdom_157, retro_mdom_706,
Mustela putorius furo	ENSMPUG00000002258	1 retrocopy	retro_mputfur_585,
Nomascus leucogenys	ENSNLEG00000009520	1 retrocopy	retro_nleu_464,
Oryctolagus cuniculus	ENSOCUG00000002670	2 retrocopies	retro_ocun_1045, retro_ocun_990,
Ochotona princeps	ENSOPRG00000004055	1 retrocopy	retro_opri_1152,
Pongo abelii	ENSPPYG00000014914	1 retrocopy	retro_pabe_613,
Pan troglodytes	ENSPTRG00000016259	1 retrocopy	retro_ptro_506,
Pteropus vampyrus	ENSPVAG00000004829	1 retrocopy	retro_pvam_475,
Sus scrofa	ENSSSCG00000009223	1 retrocopy	retro_sscr_447,
Tursiops truncatus	ENSTTRG00000004207	1 retrocopy	retro_ttru_1549,
Vicugna pacos	ENSVPAG00000004012	1 retrocopy	retro_vpac_125,