RetrogeneDB ID: retro_ptro_1758

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:16121106..16122038(+)
• 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_1758
AGCAGCATGGCGGACTACCTGATCAGCGGCAGCACCGGCTACGTGCCCAAGGATGGGCTCACTGTGCCCCAGCTCTTCGC
CGGCGCTGACGGCCTCACCCACAACGACTTGCTGATTCTTCCAGGATTCATAGACTTCATAGCTGATGAGGTGGACCTGA
CCTCAGCCCTGACCCGGAAGGTCACGCTGAAGACGCCGCTGATCTCCTCCCCTATGGACACTGTGACAGAGGCTGACATG
GCCATCGCGATGGCTCTGATGGGACGTATTGGTTTCATTCACTACAACTGTACCGCAGAGTTCCAGGCCAAGGAGGTACA
GAAGATCAAGAAGTTTGAACAGGGCTTCATCACGGACCCCGTGGTGCTGAGCCCCTCGCACACTGTGGGTGATGTGCTGG
AGGCCAAGATGCGGCATGGCTTCTCTGGCATCCCCATCACTAGACGGGCACCAAGCTGGTGGGCATCGTCACCTCCCGAG
ACACTGACTTTCTTGCTGAGAAGGACAACACCACCCTCCTCAGTGAGGTGATGACGCCAAGGATTGAGCTGGTGGTGGCT
CCAGCAGGTGTGACGTTGAAAGAGGCAAAAGAGATCCTAAGTGTAGCGAGAAAGGGAAGCTGCTTATCGTCAATGATCGC
GATTAACTGGTGGCCATCATCACCCACTCCGACCTGAAGAAGAACCGAGACTACCCTCTGGCCTCCAAGGATTCCCACAA
GCAGCTGCTGTGCAGGGCAGCTGTGGGCACCCGTGAGGATGACAAATACTGCCTGGACCTGCTCTTCCAGGCGGGTGTCA
ACGTATAGTCTTGGACTTGTCCCAGGGAACTCGGCACATCAGATCACCATGGTGCATTACATCAAACAAAAGTACCCCCA
CCTCCAGGTGACTGGGGGGAACATGGTGACAGCAGCCCAGGCCAAGAACCTG

Alignment

ORF - retro_ptro_1758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.89 %
• Parental protein coverage: 52.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ASMADYLISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISS
          .SMADYLISG.TGYVP.DGLT..QLFA.ADGLT.ND.LILPGFIDFIADEVDLTSALTRK.TLKTPLISS
Retrocopy SSMADYLISGSTGYVPKDGLTVPQLFAGADGLTHNDLLILPGFIDFIADEVDLTSALTRKVTLKTPLISS

Parental  PMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHG
          PMDTVTEADMAIAMALMG.IGFIH.NCT.EFQA.EV.K.KKFEQGFITDPVVLSPSHTVGDVLEAKMRHG
Retrocopy PMDTVTEADMAIAMALMGRIGFIHYNCTAEFQAKEVQKIKKFEQGFITDPVVLSPSHTVGDVLEAKMRHG

Parental  FSGIPITE-TGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEIL-QRSKK
          FSGIPIT..TGT...KLVGIVTSRD.DFLAEKD.TTLLSEVMTPRIELVVAPAGVTLKEA.EIL...S.K
Retrocopy FSGIPITR<TGT---KLVGIVTSRDTDFLAEKDNTTLLSEVMTPRIELVVAPAGVTLKEAKEIL<KCSEK

Parental  GKLPIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDV-IVLDS
          GKL.IVNDRD.LVAII...DLKKNRDYPLASKDS.KQLLC.AAVGTREDDKY.LDLL.QAGV.V.IVLD.
Retrocopy GKLLIVNDRD*LVAIITHSDLKKNRDYPLASKDSHKQLLCRAAVGTREDDKYCLDLLFQAGVNV<IVLDL

Parental  SQ-GNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNL
          SQ.GNS..QI.MVHYIKQKYPHLQV.GGN.VTAAQAKNL
Retrocopy SQ<GNSAHQITMVHYIKQKYPHLQVTGGNMVTAAQAKNL

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	0.30 RPM	46.92 RPM
SRP007412_cerebellum	0.25 RPM	18.03 RPM
SRP007412_heart	0.12 RPM	6.44 RPM
SRP007412_kidney	0.10 RPM	12.74 RPM
SRP007412_liver	0.07 RPM	7.14 RPM
SRP007412_testis	0.32 RPM	4.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1758 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1758 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2608
Gorilla gorilla	retro_ggor_1827

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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,
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,