RetrogeneDB ID: retro_ggor_2993

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:40969586..40971130(-)
• Located in intron of: None

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_2993
AGCATGGCGGACTACCTCATCAGCGGCGGCCCCCGCTACCAGCCCGAGGATGGGCTCACCGCACAGCAGCTCTTTGCCGG
CGCTGACGACCTCACCTACAACGATTTCCTGATTCTCCCAGGATTCATAGACTTCCTAGCTGGTGAGGTGGACCTGACCT
CAGCCCTGACCCGGAAGATCACGCTGAAGACGCCACTGATCTCCTTTCCCACGGACACTGTGATAGAGGCCGACATGGCC
ATCGCGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCACAACTGCACCCCAGAGTTCCAGGCCAACAAGGTGCAGAA
GGTCAAGAAGTTTGAACAGGGCTTCATCACAGACCCTGTGGTACTGAGCCCCTTGCACACTGTGGGTGATGTGCTGGAGG
CCAAGATGCGGCATGGCTTCTCTGGCATCCCCATCACTGAGACCGGCACCATCGGCAGCAAGCTGGTGGGCATCGTCACC
TCCCGAGACATTGACTTCCTTGCTGAGAAGGACCACACACCCTCCTCAGTGAGGTGATGACGCCAAGGATGGAGCTAGTG
GTGGCTCCAGCAGGCGTGACATTCAAAGAGGCAAATGAGATCCTGCAGCATAGCAAGAAAGGGAAGCTGCCTGTTATCAA
TGATCATGATGAGCTGGTGGCCATCATCGCCCGCACGGACCTGAAGAAGAACCGAGACTACCCTCTGGCCTCCAAGGATT
CCCACAAGCAGTTGCTGTGAGGGGCAGTTGTGGGCACCTGTGAAGATGACAAATTCCGCCTGGGCCTGCTCACCCGGGCG
GGCGTCGATGTCATAGTCTTGGACTCGTCCCAAGGGAACTTGGTGTATCAGATTGCCATGGTGCATTACATCAAACAGAA
GTACCCCCACCTCCAGGTGATTGGGGGGAATGTGGTGACAGCAGCCCAGGCCAAGAACCTGATTAACGCTGGTGTGGATG
GGCTGCACGTGGGCATGGGCTGCGGCTCCATCTGCATCACCCCGGAAGTGATGGCCTGTGGTCGGACCCACGGCACTGCT
GTGTACAAGGTGGCCGAGTATGCCTGGCGTTTTGGTGTGCCCATCATAGCTGATGGCGGCATCCAGACCATGGGGCACGT
GGTCAAGGCCCTGGCCCTTGGAGCCTCCACAGTGATGATGGGCTCCTTGCTGGCCGCCACCACGGAGGCCTCCGGTGAAT
ACTTCTTCTCAGACAGGGTGCCGCTCAAGAAGTATCAGGGCATGGGCTCTATGGATGCCATGGAGAAGAGCAGCAGCAGC
CAGAAATGATACTTCAGCGAGGCGGATAAGATGAAGTTCGCGCAGGGTATCTCGGGCTCCATCCAGGACAAAGGGTCCAT
TCAGAAGTTCGTGCCCTACCTCATAGCGGGCATCCAGCACAGTTGCCAGGATATCAGGGCCCGAAGCCTGGCTGTCCTTC
GGTCCATGATGTACTCAGGAGAGCTCAAGTTTGAGAAGCCGACCGTGTCGGCCCAGATCGAGGGTGGCGTTCGTGGCCTG
CACTCTTACGAGAAGTGGCTGTAC

Alignment

ORF - retro_ggor_2993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.73 %
• Parental protein coverage: 91.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SMADYLISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISSP
          SMADYLISGG..Y.PEDGLTAQQLFA.AD.LTYNDFLILPGFIDF.A.EVDLTSALTRKITLKTPLIS.P
Retrocopy SMADYLISGGPRYQPEDGLTAQQLFAGADDLTYNDFLILPGFIDFLAGEVDLTSALTRKITLKTPLISFP

Parental  MDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGF
          .DTV.EADMAIAMALMGGIGFIHHNCTPEFQAN.V.KVKKFEQGFITDPVVLSP.HTVGDVLEAKMRHGF
Retrocopy TDTVIEADMAIAMALMGGIGFIHHNCTPEFQANKVQKVKKFEQGFITDPVVLSPLHTVGDVLEAKMRHGF

Parental  SGIPITETGTMGSKLVGIVTSRDIDFLAEKDHT-TLLSEVMTPRIELVVAPAGVTLKEANEILQRSKKGK
          SGIPITETGT.GSKLVGIVTSRDIDFLAEKDHT.TLLSEVMTPR.ELVVAPAGVT.KEANEILQ.SKKGK
Retrocopy SGIPITETGTIGSKLVGIVTSRDIDFLAEKDHT<TLLSEVMTPRMELVVAPAGVTFKEANEILQHSKKGK

Parental  LPIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQG
          LP..ND.DELVAIIARTDLKKNRDYPLASKDS.KQLL.GA.VGT.EDDK.RL.LLT.AGVDVIVLDSSQG
Retrocopy LPVINDHDELVAIIARTDLKKNRDYPLASKDSHKQLL*GAVVGTCEDDKFRLGLLTRAGVDVIVLDSSQG

Parental  NSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVY
          N.VYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLI.AGVDGL.VGMGCGSICIT.EVMACGR..GTAVY
Retrocopy NLVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLINAGVDGLHVGMGCGSICITPEVMACGRTHGTAVY

Parental  KVAEYARRFGVPIIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLD
          KVAEYA.RFGVPIIADGGIQT.GHVVKALALGASTVMMGSLLAATTEA.GEYFFSD.V.LKKY.GMGS.D
Retrocopy KVAEYAWRFGVPIIADGGIQTMGHVVKALALGASTVMMGSLLAATTEASGEYFFSDRVPLKKYQGMGSMD

Parental  AMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARSLSVLRSMMYSGEL
          AMEKSSSSQK.YFSE.DK.K.AQG.SGSIQDKGSIQKFVPYLIAGIQH.CQDI.ARSL.VLRSMMYSGEL
Retrocopy AMEKSSSSQK*YFSEADKMKFAQGISGSIQDKGSIQKFVPYLIAGIQHSCQDIRARSLAVLRSMMYSGEL

Parental  KFEKRTMSAQIEGGVHGLHSYEKRLY
          KFEK.T.SAQIEGGV.GLHSYEK.LY
Retrocopy KFEKPTVSAQIEGGVRGLHSYEKWLY

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	0.00 RPM	30.79 RPM
SRP007412_cerebellum	0.00 RPM	31.20 RPM
SRP007412_heart	0.00 RPM	12.45 RPM
SRP007412_kidney	0.00 RPM	10.79 RPM
SRP007412_liver	0.03 RPM	6.25 RPM
SRP007412_testis	0.52 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_2993 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2993 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4808
Pan troglodytes	retro_ptro_3198
Pongo abelii	retro_pabe_3736
Macaca mulatta	retro_mmul_317

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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,