RetrogeneDB ID: retro_ptro_2886

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:34544845..34546380(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSPTRG00000019660
• Aliases: None
• Description: Inosine-5'-monophosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:H2QVB7]

Sequence

>retro_ptro_2886
AGCGTGGTGGACTACCTGATCAGCGGTGGCACCGGCTACATGCCCGAGGACGGGCTCATCGAGCAGCAGCTCTTCGCCAG
CGCCTAAGGCCTCACCTAGGACGCCTTCCTGATTCTCCCAGGACTCATAGACTTCATAGCTGAGGTGGACCTTACCTCAG
CCCTGACCCGGAAGATCACGCTGAAGACACCGCTGATCTCCTCCCCCATGGACACTGTGACAGAGGCTGACGTGGCCATC
GCGATGGCTCTGATGGGAGATACTGGTTTCATTCACCACAACTGCACCCCAGAGCTCCAGGCCAAGGAGCTACGGAAGGT
CAAGAAGTTTGAACAGGGCTTCATCACGGACCCCACGGTGCTGAGCCCCTCCCACACTGTAGGTGATGTGCTGGAGGCCA
AGATGCGGCATGGCTTCTCTGGCATCCCCATCACTGAGACGGGCACCATGGGCAGCAAGCTGGTGGGCATCGTCGCCTCC
CGAGACATCAACTTTCTTGCTGAGAAGGACCACACCACCCTCCTCAGTGAGGTGATGACGCCAAGGCTCGAGCTGGTGGT
GGCTCCAGCATGTGTGACGTTGAAAGAGGCAAATGAGATCCTGCAGCGTAGCAAGAAAGGGAAGCTGCCTATCATCAATG
ATCGCAATGAGCTGGTGGCCATTATCACCGGCAGCGACCTGAAGAAGAACCAAGACTACCCTCTGGCCTCCAAGGATTCC
CACAAGCAGCTGCTGTGCGGGGCAGCTGTGGGCACCCGTGAGGATGACAAATATCGCCTGGACCTGCTCACCCAGGTGGG
CGTCGACGTCATAGTCTTGGACTCATCCCAAGGGAACTTGGTGTATCAGATCGCCATGGTGCATTACATCAAACAGAAGT
ACCCCCACCTCCAGGTGATTGGCAGGAACATGGTGACAGCAGCCCAGGCCAAGAACCTGATTGACGCTGGTGTGGACGGG
CTGTGTGTGGGCATGGGCTGCAGCTCCATCTGCGTCACCTGGGAATTGATGGCTTGTGGTCAGCCCCAGGGCACTGCTGT
GTACAAGGAGGCCAAGTATGCCCGGCGCTTTGGGTGCCCATCATAGCCAATGGCGGCATCCAGACCATGGGGCACATAGT
CAAGGCCCTGGCCCTTGGAGTCTCCACAGTGATGATGGGCTCCCTGCTGGCCATCACCACGGAGGCCCCTGGTGAGTACT
TCTCAGACGAGGTGCGGCTCAAGAAGTACTGGGGCATGGGCTCACTGGATGCCATGGAGAAGAGCAGCAGCCAGAAACGA
TACTTCAGCAAGGGGGATAAGGTGAAGATCGTGCAGGGTGTCTTGGGCTCCATCCAGGACAAAGGGTCCATTCAGAAGTT
CGTGCCCTACCTCATAGTGGGCATCCAGCACGGCTGCCAGGGTATCGGGGCCCACAGCCTGTCTGTCCCTCGGTCCATGA
TGTACTCAGGAGAGCTCAAGTTTGAGAAGCGGATCATGTCGGCCCAGATCGAGGGTGGCGTCCATGGTCTGCACTTTTAT
GAAAAGCGGCTGTAC

Alignment

ORF - retro_ptro_2886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 85.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SMADYLISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISSP
          S..DYLISGGTGY.PEDGL..QQLFASA.GLT...FLILPG.IDFIA.EVDLTSALTRKITLKTPLISSP
Retrocopy SVVDYLISGGTGYMPEDGLIEQQLFASA*GLT*DAFLILPGLIDFIA-EVDLTSALTRKITLKTPLISSP

Parental  MDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGF
          MDTVTEAD.AIAMALMG..GFIHHNCTPE.QA.E.RKVKKFEQGFITDP.VLSPSHTVGDVLEAKMRHGF
Retrocopy MDTVTEADVAIAMALMGDTGFIHHNCTPELQAKELRKVKKFEQGFITDPTVLSPSHTVGDVLEAKMRHGF

Parental  SGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQRSKKGKL
          SGIPITETGTMGSKLVGIV.SRDI.FLAEKDHTTLLSEVMTPR.ELVVAPA.VTLKEANEILQRSKKGKL
Retrocopy SGIPITETGTMGSKLVGIVASRDINFLAEKDHTTLLSEVMTPRLELVVAPACVTLKEANEILQRSKKGKL

Parental  PIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGN
          PI.NDR.ELVAII...DLKKN.DYPLASKDS.KQLLCGAAVGTREDDKYRLDLLTQ.GVDVIVLDSSQGN
Retrocopy PIINDRNELVAIITGSDLKKNQDYPLASKDSHKQLLCGAAVGTREDDKYRLDLLTQVGVDVIVLDSSQGN

Parental  SVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYK
          .VYQIAMVHYIKQKYPHLQVIG.N.VTAAQAKNLIDAGVDGL.VGMGC.SIC.T.E.MACG.PQGTAVYK
Retrocopy LVYQIAMVHYIKQKYPHLQVIGRNMVTAAQAKNLIDAGVDGLCVGMGCSSICVTWELMACGQPQGTAVYK

Parental  VAEYARRFG-VPIIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLD
          .A.YARRFG.VPIIA.GGIQT.GH.VKALALG.STVMMGSLLA.TTEAPGEY.FSD.VRLKKY.GMGSLD
Retrocopy EAKYARRFG<VPIIANGGIQTMGHIVKALALGVSTVMMGSLLAITTEAPGEY-FSDEVRLKKYWGMGSLD

Parental  AMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARSLSVLRSMMYSGEL
          AMEK.SSSQKRYFS.GDKVKI.QGV.GSIQDKGSIQKFVPYLI.GIQHGCQ.IGA.SLSV.RSMMYSGEL
Retrocopy AMEK-SSSQKRYFSKGDKVKIVQGVLGSIQDKGSIQKFVPYLIVGIQHGCQGIGAHSLSVPRSMMYSGEL

Parental  KFEKRTMSAQIEGGVHGLHSYEKRLY
          KFEKR.MSAQIEGGVHGLH.YEKRLY
Retrocopy KFEKRIMSAQIEGGVHGLHFYEKRLY

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	0.29 RPM	46.92 RPM
SRP007412_cerebellum	0.25 RPM	18.03 RPM
SRP007412_heart	0.03 RPM	6.44 RPM
SRP007412_kidney	0.31 RPM	12.74 RPM
SRP007412_liver	0.13 RPM	7.14 RPM
SRP007412_testis	0.21 RPM	4.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2886 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2886 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4247
Pongo abelii	retro_pabe_3392

---

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,
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	ENSPTRG00000014908	1 retrocopy	retro_ptro_501,
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,