RetrogeneDB ID: retro_ggor_2688

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:123156140..123157695(+)
• 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_2688
TTGGGTCGCCGGGTCTCTGGCAGCCTGACAGACTACCTGATGAGCCGGGGCACCGGCTGCATGCCCGAGGATGGGCTCAC
CACGCAGCAGCTCTTCGCCAGAGCCGACAGCCTCACCTACAACGAGTTCCTGATTCTCCCAGGATTCATAGACTTCATAG
CTGATGAAGCGGACCTGACCTCAGCCCTTACCTGGAAGATCACGCTGAAGACGCCGCTGATCTCCTCCTCCATGGACACT
GTGACAGAGGGCAACATGGCCATCACGATGGCTCTGGTGGGAGGTATTGGTTTCATTCACCACAACTGCACCCCAGAGTT
CTAGGCCAAGGAGGTGTGGAAGGTCAAGAAGTTTGAACATGGCTTCATCACGGACCCCATGGTGCTGAGCCCCTCGCACC
CTGTGGGTGATGTGCTGGAGGCCACGATGCGGCATGGCTTCTCTGGTATCCCCATCACTGAGACAGGCACCATGGGCAGC
AAGCCGGTGGGCATCGTCACCTCCCAAGACATCGACTTTCTTGCTGAGAAGGACCACACCACCCTCCTCAGTGAGGTGAT
GATGCCAAGGTTTGAGCTGGTGGTGGCTCCAGCAGGAGTGATGTTGAAAGAGGCAAATGAGATCCTGCAGCAAAGCAAGA
AAGTGAAGCTGCCTATCGTCAATGATGACGATGAGCTGGTGGTCATCATTGTCCTCACTGACCTGAAGAACTGAGACTAC
CCTGTGGCCTCCAAGGATTCCCATGAGCAGCTGCTGTGTGGGGCAGCTGTGGGCACCTGTGAGGATGACAAATACCGCCT
GGACCTGCTCACCCAGGCGGGTGTCGACGTCATAGTCTTGGACTTGTCCGAAGGGAACTTGCTGTATCAACTGCCATGGT
GTATTACATCAAACAGAAGTACTCCCACCTCCAGGTGATTGTGGGGAACGTGGTGACAGCAGCCCAGGCCAAGAACCTGA
TTGACGCTGGTGTGGACGGGCTGTGTGTGGGAATAGGCTGCGGCTCCCTCTGCATCACCCAGGAAGTGATGGCATGTGGT
TGCCCCCAGGGCACTGTGTGTACAAGGTGGCTGAGTATGCCCGGCACTTTGGTGTGCGCATCATAGCCGATGGTGGCATC
CTGACTGTGGGGCACGTCAAGGTGCTGGCCCTTGGTGCCTCCATAGTGATGACGGGCTCCCTGCTGGCTGCCACCTCAGA
GGCCCCCAGCGAATAGTTCTCAGATGGGGTGTGGCTCAAGAAATACTGGGGCACAGGCTTGCTGGATGCCATGGAGAAGA
GCAGCAGCAGCCAGGAACGATACTTCAGTGAGGGGGATAAGGTGAAGATCACACAGGGTGTCTCGGGCTCCATCCAGGAC
AAAGGGTCCATTCAGAAGTTCATGCCCTACCTCATAGTGGGCATCCAGCATGGCTGCCAAGATATCAGGGCCCGCAGCCT
GTCTGTCCTTTGGTCCATAATGTACGCAGGAGAGCTCAAGTTTGAGAAGCGTACCATGTCGGCCCAGATTGAGGGTGGCG
TCCATGGCCTGCACTCTTAGGAGAAGCGGCTGTAC

Alignment

ORF - retro_ggor_2688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 87.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGRLRRASMADYLISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLK
          .GR....S..DYL.S.GTG..PEDGLT.QQLFA.AD.LTYN.FLILPGFIDFIADE.DLTSALT.KITLK
Retrocopy LGRRVSGSLTDYLMSRGTGCMPEDGLTTQQLFARADSLTYNEFLILPGFIDFIADEADLTSALTWKITLK

Parental  TPLISSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLE
          TPLISS.MDTVTE..MAI.MAL.GGIGFIHHNCTPEF.A.EV.KVKKFE.GFITDP.VLSPSH.VGDVLE
Retrocopy TPLISSSMDTVTEGNMAITMALVGGIGFIHHNCTPEF*AKEVWKVKKFEHGFITDPMVLSPSHPVGDVLE

Parental  AKMRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQ
          A.MRHGFSGIPITETGTMGSK.VGIVTS.DIDFLAEKDHTTLLSEVM.PR.ELVVAPAGV.LKEANEILQ
Retrocopy ATMRHGFSGIPITETGTMGSKPVGIVTSQDIDFLAEKDHTTLLSEVMMPRFELVVAPAGVMLKEANEILQ

Parental  RSKKGKLPIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIV
          .SKK.KLPIVND.DELV.II..TDL.KN.DYP.ASKDS..QLLCGAAVGT.EDDKYRLDLLTQAGVDVIV
Retrocopy QSKKVKLPIVNDDDELVVIIVLTDL-KN*DYPVASKDSHEQLLCGAAVGTCEDDKYRLDLLTQAGVDVIV

Parental  LDSSQGNSVYQI-AMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGR
          LD.S.GN..YQ..AMV.YIKQKY.HLQVI.GNVVTAAQAKNLIDAGVDGL.VG.GCGS.CITQEVMACG.
Retrocopy LDLSEGNLLYQL<AMVYYIKQKYSHLQVIVGNVVTAAQAKNLIDAGVDGLCVGIGCGSLCITQEVMACGC

Parental  PQGT-AVYKVAEYARRFGVPIIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKK
          PQGT..VYKVAEYAR.FGV.IIADGGI.TVGH.VK.LALGAS.VM.GSLLAAT.EAP.E..FSDGV.LKK
Retrocopy PQGT<CVYKVAEYARHFGVRIIADGGILTVGH-VKVLALGASIVMTGSLLAATSEAPSE-*FSDGVWLKK

Parental  YRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARSLSVLR
          Y.G.G.LDAMEKSSSSQ.RYFSEGDKVKI.QGVSGSIQDKGSIQKF.PYLI.GIQHGCQDI.ARSLSVL.
Retrocopy YWGTGLLDAMEKSSSSQERYFSEGDKVKITQGVSGSIQDKGSIQKFMPYLIVGIQHGCQDIRARSLSVLW

Parental  SMMYSGELKFEKRTMSAQIEGGVHGLHSYEKRLY
          S.MY.GELKFEKRTMSAQIEGGVHGLHS.EKRLY
Retrocopy SIMYAGELKFEKRTMSAQIEGGVHGLHS*EKRLY

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	0.08 RPM	31.20 RPM
SRP007412_heart	0.16 RPM	12.45 RPM
SRP007412_kidney	0.04 RPM	10.79 RPM
SRP007412_liver	0.11 RPM	6.25 RPM
SRP007412_testis	0.10 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_2688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2688 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4005
Pan troglodytes	retro_ptro_2719

---

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,