RetrogeneDB ID: retro_ggor_1798

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:89571706..89572630(-)
• Located in intron of: ENSGGOG00000010972

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSGGOG00000003963
• Aliases: None
• Description: Inosine-5'-monophosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G3QMZ1]

Sequence

>retro_ggor_1798
GCGCAGCAGCTCTTCGCCAGCGACGAGGGACTCACCTACAACGACTTCTTGATTCTCCCAGGATTCATAGACTTCATAGC
TGATGAGGTGGACCTGACCTCAGCCCTGACCCAATGGTCACGCTGAAGACGCTGCTGATCTCCTCCCCCATGGACACTGT
GACAGAGGCCGACGTGGCCATCGTGATGGCTCTGATGGGAGGTACTGGTTTCATTCACCACAACTGCACCCCAGAGTTCC
AGGCCAGTGAGGTGCAGAAGCTCAAGAAGTTTGAACAGGGCTTTATCACACACCCCGTGGTGCTGAGCCCCTTGCACACT
GTGGGTGATGTGCTGGAGGCCAAGATGCATCATGGCTTCTCTAGCATCCCCATCACTGAGACGGGCACCATGGGCAGCAA
GCTGGTGGGCATCGTCACCTCCCGAGACATCGACTTTCTTGCTGAGAAGGACCGTACCACCCTCCTCAGTGAGGTGATGA
TGCCAAGGATCAAGCTAGTGGTGGCTCCAGCAGTGTGAGGTTTAAAGAGGCAAATGAGATCCTGCAGCTTAGCAAGAAAG
GAAGCTGCCTATCGTCAATGATCGCGATGAGCTGGTGGCCATTATCACCTGCACCGCCCTGAAGAACCGAGACTACCCTG
TGGCCTCCAAGGATTCCCACGAGCAGCTGCTGGGCGGGGCAGCTGTGGGTACCCATGAGGATGACAAATACCGCCTGGAC
CTGCTCACCCAGGTGGGCATCGATGTCGTAGGCTTGGACTCGTCCCAAGGGAACTCGGTGTATCAGGTCGCCATGGTGCA
TTACATCAAACAAAAGTAACCCCACCTCCAGGTGGTTGGGGGGAACGTGGTGAGAGCAGCCCAGGCCAACAACCTGATTG
ACGCTGGTGTGGATGGGCTGGGCAGGGGCATGGACTGCGCGGCT

Alignment

ORF - retro_ggor_1798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.35 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTR-KITLKTPLISSPMDTVTEADMAIAMALMGGI
          AQQLFAS..GLTYNDFLILPGFIDFIADEVDLTSALT....TLKT.LISSPMDTVTEAD.AI.MALMGG.
Retrocopy AQQLFASDEGLTYNDFLILPGFIDFIADEVDLTSALTQ<MVTLKTLLISSPMDTVTEADVAIVMALMGGT

Parental  GFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIV
          GFIHHNCTPEFQA.EV.K.KKFEQGFIT.PVVLSP.HTVGDVLEAKM.HGFS.IPITETGTMGSKLVGIV
Retrocopy GFIHHNCTPEFQASEVQKLKKFEQGFITHPVVLSPLHTVGDVLEAKMHHGFSSIPITETGTMGSKLVGIV

Parental  TSRDIDFLAEKDHTTLLSEVMTPRIELVVAPA-GVTLKEANEILQRSKKG-KLPIVNDRDELVAIIARTD
          TSRDIDFLAEKD.TTLLSEVM.PRI.LVVAPA..V..KEANEILQ.SKKG.KLPIVNDRDELVAII..T.
Retrocopy TSRDIDFLAEKDRTTLLSEVMMPRIKLVVAPA<SVRFKEANEILQLSKKG<KLPIVNDRDELVAIITCTA

Parental  LKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIKQKYPH
          L.KNRDYP.ASKDS..QLL.GAAVGT.EDDKYRLDLLTQ.G.DV..LDSSQGNSVYQ.AMVHYIKQK.PH
Retrocopy L-KNRDYPVASKDSHEQLLGGAAVGTHEDDKYRLDLLTQVGIDVVGLDSSQGNSVYQVAMVHYIKQK*PH

Parental  LQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGS
          LQV.GGNVV.AAQA.NLIDAGVDGL..GM.C..
Retrocopy LQVVGGNVVRAAQANNLIDAGVDGLGRGMDCAA

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	0.72 RPM	30.79 RPM
SRP007412_cerebellum	0.32 RPM	31.20 RPM
SRP007412_heart	2.66 RPM	12.45 RPM
SRP007412_kidney	3.72 RPM	10.79 RPM
SRP007412_liver	5.28 RPM	6.25 RPM
SRP007412_testis	2.59 RPM	21.76 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_1798 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1798 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2368
Pongo abelii	retro_pabe_2138

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017770	1 retrocopy	retro_cjac_2045,
Homo sapiens	ENSG00000106348	7 retrocopies	retro_hsap_2360, retro_hsap_2368, retro_hsap_2608, retro_hsap_3797, retro_hsap_4005, retro_hsap_4247, retro_hsap_4808,
Gorilla gorilla	ENSGGOG00000003963	6 retrocopies	retro_ggor_1790, retro_ggor_1798 , retro_ggor_1827, retro_ggor_2551, retro_ggor_2688, retro_ggor_2993,
Gorilla gorilla	ENSGGOG00000013245	1 retrocopy	retro_ggor_594,
Macropus eugenii	ENSMEUG00000016082	2 retrocopies	retro_meug_2095, retro_meug_542,
Macaca mulatta	ENSMMUG00000014509	2 retrocopies	retro_mmul_1551, retro_mmul_317,
Nomascus leucogenys	ENSNLEG00000012341	1 retrocopy	retro_nleu_2508,
Pongo abelii	ENSPPYG00000017976	7 retrocopies	retro_pabe_2133, retro_pabe_2138, retro_pabe_2346, retro_pabe_3102, retro_pabe_3292, retro_pabe_3392, retro_pabe_3736,
Pan troglodytes	ENSPTRG00000019660	7 retrocopies	retro_ptro_1087, retro_ptro_1724, retro_ptro_1758, retro_ptro_2575, retro_ptro_2719, retro_ptro_2886, retro_ptro_3198,