RetrogeneDB ID: retro_ggor_602

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:104275546..104276574(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT9
• Ensembl ID: ENSGGOG00000014777
• Aliases: None
• Description: None

Sequence

>retro_ggor_602
ATGGCTGGATGCCACCTGTCCAAGGCTTTAGCGACCGTGTCTCCCTTCATGACCTTGGCCTCTGTGACAGGCAGGCCCGG
CAGCTGCCCCAACATCCCGGCCAGCTGGAGTCTGTTTTCCTCACATAGGTTTTCTCTAAACTTCATCACCTCAGGTTCGA
AGCGCACTGCTGAGAAGCCCCACGAGAAGGCCCGGACATCTCCGTACCCTGGCTCCAGGGTGGAGCGAAGCCTGGTTCCC
CATGAGAAAGTGAGCTGGCTGGTCGAGTGGCGAGAGTAACGCCCGTGGAGTACACTGCCAGCTCTGTCTTGCCTGGGCCC
GTGTGGGCAGACCCTCAAGTGGGTGAAAGGAACTTGTCTCCTAAGTTTAACGAAAAGGATGGGCATGTGGAGAGAAGGAA
CCAGCATGGCTTGTATGAGATTGAGAAGGGTAGACTTAGAAATCCTGCACCTCGGACAGGACTGGTTGGCCAAGGGCCTC
TGGGGTGTTGGGACCCCAATCATGCTGTAGATCCCATCTTAACCAGATGGAAAAGGGATAGCAAGGGAAACGAAATTACC
CACCCTATTTCTGGAAAAAATATCCTGCAATTTGTAGCCATCAAAAGGAAGGACTGTGGAGAATAGGCAATCCCAGGGGG
TATGGTGGATCCAGGAGAGAAAATTAGTGCTACACTGAAGAGAGAATTTGGCGAGGAAGCCATGAACTCTTTACAGAAAT
CTAGGAAAGAAATGCAGGAGTTGGAGAGACAATTGCACAAACTCCTCAGTCAGGAACATTTTGTGGTCTATAAAGGCTAC
GTGGATGATTCTAGAAACACAGATAACTGCTGGATAGAGACAGAGGCTGTGAACTACCGTGATGAAATAATGGACCATCT
TCCTCTGGAAGCTGGCGATGATGCCAAGAAAGTGAAATGGGTGGACATTAATGATAAACTTGAGCTTTATGCCAGCCTCT
CCCAATTTATTCAACTTGTGGCTGAGAAATGAGGTGCCCACTGATGTAAGGATATGTATCCTGATTGC

Alignment

ORF - retro_ggor_602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.24 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGRLVGKALAAVSLSLALASVTIRSSGCRGIPAFRNSFSSSWFHLNTNVMSGSNGSKENSHNKARTSPY
          MAG....KALA.VS....LASVT.R...C..IPA....FSS..F.LN....SGS....E..H.KARTSPY
Retrocopy MAGCHLSKALATVSPFMTLASVTGRPGSCPNIPASWSLFSSHRFSLNF-ITSGSKRTAEKPHEKARTSPY

Parental  PGSKVERSQVPNEKVGWLVEWQD-YNPVEYTAVSVLAGPRWADPQIREGSFSSETPSQKNKQQKLERSVK
          PGS.VERS.VP.EKV.WLVEW.....PVEYTA.SVL.GP.WADPQ..E...S...P....K....ER...
Retrocopy PGSRVERSLVPHEKVSWLVEWRE<VTPVEYTASSVLPGPVWADPQVGERNLS---PKFNEKDGHVERRNQ

Parental  ISMYQIKPNFSRNPAGRTGLVGRGLLGRWGPNHAADPIITRWKRDSSGNKIMHPVSGKHILQFVAIKRKD
          ...Y.I.....RNPA.RTGLVG.G.LG.W.PNHA.DPI.TRWKRDS.GN.I.HP.SGK.ILQFVAIKRKD
Retrocopy HGLYEIEKGRLRNPAPRTGLVGQGPLGCWDPNHAVDPILTRWKRDSKGNEITHPISGKNILQFVAIKRKD

Parental  CGEWAIPGGMVDPGEKISATLKREFVEEALNSLQKTSAEKREIEEKLHKLFSQDHLVIYKGYVDDPRNTD
          CGE.AIPGGMVDPGEKISATLKREF.EEA.NSLQK...E..E.E..LHKL.SQ.H.V.YKGYVDD.RNTD
Retrocopy CGE*AIPGGMVDPGEKISATLKREFGEEAMNSLQKSRKEMQELERQLHKLLSQEHFVVYKGYVDDSRNTD

Parental  NAWMETEAVNYHDETGDIMDNLTLEAGDDAGKVKWVDINDKLKLYASHSQFIKLVAEKRDAHWSEGSEAD
          N.W.ETEAVNY.DE...IMD.L.LEAGDDA.KVKWVDINDKL.LYAS.SQFI.LVAEK..AH.......D
Retrocopy NCWIETEAVNYRDE---IMDHLPLEAGDDAKKVKWVDINDKLELYASLSQFIQLVAEK*GAH*CKDMYPD

Parental  C
          C
Retrocopy C

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	2.83 RPM	31.79 RPM
SRP007412_cerebellum	1.26 RPM	18.08 RPM
SRP007412_heart	1.16 RPM	10.54 RPM
SRP007412_kidney	0.86 RPM	39.34 RPM
SRP007412_liver	0.61 RPM	18.81 RPM
SRP007412_testis	15.64 RPM	34.60 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_602 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_602 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_709
Pan troglodytes	retro_ptro_506
Pongo abelii	retro_pabe_613
Callithrix jacchus	retro_cjac_1047
Oryctolagus cuniculus	retro_ocun_990
Bos taurus	retro_btau_1112
Sus scrofa	retro_sscr_447
Canis familiaris	retro_cfam_1271
Equus caballus	retro_ecab_123

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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,