RetrogeneDB ID: retro_ptro_2575

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:139931397..139932957(+)
• 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_2575
CGCGGCAGCATGGCAGACTACCTGATCAGAGGCGGCACCAGCTACATGCCCGAGGATGGGCTCATGGCGCAGCAGCTCTT
CACTGGTGCAGCAGCTCGCGACGGCCTCACCTACAACAACTTCCTGATTCTCCCAGGATTCATAGACTTCATAGCTGATA
AGTTGGACCTGACCTCAGCCCTGACTTGGAAGATCACGCTGAAGATGCCACTGATCTCCTCCCCCATGGACGCTGTGACA
GAAGCTGACATGGCCATCGCAATGGCTCTGATGGGAGGTATTGGTTTCATTCACCACCACTGCACCCCAGAGTTCCAGGC
CAATGAGGTGCAGAAGGTCAAGAAGTTTGAACGGGGCTTTATCATGGACCCCGTGGTACTAAGCCCCTCACACACCGTGG
GTGATGTGCTGGAGGCCAAGATGCGGCATGGCTTCTCGGGCATCCCCATCACTGAGACAGGCACCATGGGCAGCAAGCTG
GTGGACATCGTCACCTCCTGAGACATCAACTTTCTTGCTGAGAAGGACCACATCACCCTCCTCAGTGAGGTGATGACACC
AAGGATTGAGCTGCTGGTGGCTCCAGCAGGTGTGATGTTGAAAGAGGCAAATGAGATCCTGCAGCCGTAGCAAGAAAGGG
AAGCTGCCTATCGTCAATGATCACAATGAGCTGGTGGCCATCATCGCCCACACCAACATGAAGAAGAACTGAGACTACCC
TCTGGCCTCCAAGGATTCCCACAAGCAGCTGCTGTGCAGGGCAGCTGTGGGCACCCGTGAGGATGACAAATACCGCCTGG
ACCTGCTCACCCAGATGGGCGTTGACATCATAGTCTTGGACTTGTCCCAAGGGAACTCATTGTATCAGATGGCCATGGTG
TATTACATCAAACAGAAGTACCCCCACCTCCAGGTGATTGGGGGGAACATGGTGACAGCAGCCCAGGCGAAGAACCTGAT
TGACACTGGTGTGGAAGGGCTGCACGTGGGCATGGGCTGCAGCTCCATCTGCATCACCCAGGAAGTGATGGCCTACAGCT
GGCCCCAGGGCACTGCTGTGTACAAGGTGGCCGAGTATGCCCGGCACTTTGGTGTGCCTACATAGCCGATGGCAGCATCC
AGACCATGGGGAACATGGTCAAGGCCCTGGCCCTTGGATCCTCCACAGTGATGATGGGCTCCCTTCTGGCCGCCACCACG
GAGGTCCCCAGCAAGTACTTCTTCTCAGATGGGGTGTGGCTCAAGAAGTACGGGGGTATGGGCTCACTGGATGCCCTGGA
GAAGAGCAGCAGCAGCCAGAAACAATACTTCATGGAGGGGGATAAGGTGAAGATCGCGCAGGGTGTCTCCAGCTCCATCC
AGGACAAAGGGTCCATTCAGAAGTTCGTGTCCTACCTCATAGCGGGCATCCAGCATGGCTGCCAGGATACTGGGGTCTGC
AACCTGTCTGTCCTTTTGTCCATGATGTACTCAGGAGAGTGCAAGTTTGAGAAGTGGACCATGTTGGCCCAGATCAAGGG
TGGCGTCCAAGGCCTGCACTCTTACAAGAAGAGGCTGTAC

Alignment

ORF - retro_ptro_2575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.06 %
• Parental protein coverage: 86.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RASMADYLISGGTGYVPEDGLTAQQLFASA---DGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTP
          R.SMADYLI.GGT.Y.PEDGL.AQQLF..A...DGLTYN.FLILPGFIDFIAD..DLTSALT.KITLK.P
Retrocopy RGSMADYLIRGGTSYMPEDGLMAQQLFTGAAARDGLTYNNFLILPGFIDFIADKLDLTSALTWKITLKMP

Parental  LISSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAK
          LISSPMD.VTEADMAIAMALMGGIGFIHH.CTPEFQANEV.KVKKFE.GFI.DPVVLSPSHTVGDVLEAK
Retrocopy LISSPMDAVTEADMAIAMALMGGIGFIHHHCTPEFQANEVQKVKKFERGFIMDPVVLSPSHTVGDVLEAK

Parental  MRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQ-R
          MRHGFSGIPITETGTMGSKLV.IVTS.DI.FLAEKDH.TLLSEVMTPRIEL.VAPAGV.LKEANEILQ.R
Retrocopy MRHGFSGIPITETGTMGSKLVDIVTS*DINFLAEKDHITLLSEVMTPRIELLVAPAGVMLKEANEILQ>R

Parental  SKKGKLPIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVL
          SKKGKLPIVND..ELVAIIA.T..KKN.DYPLASKDS.KQLLC.AAVGTREDDKYRLDLLTQ.GVD.IVL
Retrocopy SKKGKLPIVNDHNELVAIIAHTNMKKN*DYPLASKDSHKQLLCRAAVGTREDDKYRLDLLTQMGVDIIVL

Parental  DSSQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQ
          D.SQGNS.YQ.AMV.YIKQKYPHLQVIGGN.VTAAQAKNLID.GV.GL.VGMGC.SICITQEVMA...PQ
Retrocopy DLSQGNSLYQMAMVYYIKQKYPHLQVIGGNMVTAAQAKNLIDTGVEGLHVGMGCSSICITQEVMAYSWPQ

Parental  GTAVYKVAEYARRFGVP-IIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYR
          GTAVYKVAEYAR.FGVP..IADG.IQT.G..VKALALG.STVMMGSLLAATTE.P..YFFSDGV.LKKY.
Retrocopy GTAVYKVAEYARHFGVP<YIADGSIQTMGNMVKALALGSSTVMMGSLLAATTEVPSKYFFSDGVWLKKYG

Parental  GMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARSLSVLRSM
          GMGSLDA.EKSSSSQK.YF.EGDKVKIAQGVS.SIQDKGSIQKFV.YLIAGIQHGCQD.G...LSVL.SM
Retrocopy GMGSLDALEKSSSSQKQYFMEGDKVKIAQGVSSSIQDKGSIQKFVSYLIAGIQHGCQDTGVCNLSVLLSM

Parental  MYSGELKFEKRTMSAQIEGGVHGLHSYEKRLY
          MYSGE.KFEK.TM.AQI.GGV.GLHSY.KRLY
Retrocopy MYSGECKFEKWTMLAQIKGGVQGLHSYKKRLY

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	46.92 RPM
SRP007412_cerebellum	0.00 RPM	18.03 RPM
SRP007412_heart	0.00 RPM	6.44 RPM
SRP007412_kidney	0.00 RPM	12.74 RPM
SRP007412_liver	0.00 RPM	7.14 RPM
SRP007412_testis	0.00 RPM	4.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2575 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2575 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3797
Pongo abelii	retro_pabe_3102

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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,