RetrogeneDB ID: retro_pabe_2346

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:131682008..131682955(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSPPYG00000017976
• Aliases: None
• Description: IMP (inosine 5'-monophosphate) dehydrogenase 1 [Source:HGNC Symbol;Acc:6052]

Sequence

>retro_pabe_2346
CGCAGCAGCATGGCGGACTACCTGATCAGCGGCAGCACCAGCTACGTGCGCAAGGATGGGCTCACTGCGCCCCAGCTCTT
CGCCAGCGCTGACGGCCTCACTCACAACAACTTCCTGATTCTCCTAGGATTCATAGACTTCATAGCTGATGAGGTGGACC
TGACCTCAGCCCTGAACCGGAAGGTCACGCTGAAGACGCCGCTGATCTCCTCCCCTATGGACACTGTGACAGAGGCTGAC
ATGGCCATCGCGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCACAACTGCACCGCAGAGTTCCAGGCCAACGAGGT
GCGGAAGATCAAGAAGTTTGAACAGGGCTTCATCACGGACCCCGTGGTGCTGAGCCCCTCGGACACTGTGGGTGATGTGC
TGGAGGCCAAGATGCGGCATGGCTTCTCTGGCATCCGCATCACTAGACGGGCACCATAGGCAGCAAGCTATTGGGCATTG
TCACCTCCCAAGACACTGACTTTCTTGCTGAGAAGGACACCACCACCCTCCTCAGCGAGGTGATGACGCCAAGGATTGAG
CTGGTGGTGGCTCCAGCAGGTGTGACGTTGAAAGAGGCAAAAGAGATCCTAAGTGTAGCGAGAAAGGGAAGCTGCCTATC
GTCAATGATCGCGATGAACTGGTGGCCATCATCACCCACACCGACCTGAAGAAGAACTGAGACTACCCTCTGGCCTCCAA
GGATTCCCACAAGCAGCTGCTGTGCAGGGCAGCTGTGGGCACCCGTGAGGATGAAAAATACTGCCTGGACCTGCTCTCCC
AGGCGGGCGTCAACATATAGTCTTGGACTCGTCCCAGGGAACTCGGCATATCAGATCACCATGGTGCATTACATCAAACA
AAAGTACCCCCACCTCCAGGTGATTGGGGGGAACATGGTGACAGCAGCCCAGGCCAAGAACCTGATG

Alignment

ORF - retro_pabe_2346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.67 %
• Parental protein coverage: 53.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RASMADYLISGGTGYVPEDGLTEQKNFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLIS
          R.SMADYLISG.T.YV..DGLT....FASADGLT.N.FLIL.GFIDFIADEVDLTSAL.RK.TLKTPLIS
Retrocopy RSSMADYLISGSTSYVRKDGLTAPQLFASADGLTHNNFLILLGFIDFIADEVDLTSALNRKVTLKTPLIS

Parental  SPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRH
          SPMDTVTEADMAIAMALMGGIGFIHHNCT.EFQANEVRK.KKFEQGFITDPVVLSPS.TVGDVLEAKMRH
Retrocopy SPMDTVTEADMAIAMALMGGIGFIHHNCTAEFQANEVRKIKKFEQGFITDPVVLSPSDTVGDVLEAKMRH

Parental  GFSGIPITE-TGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEIL-QRSK
          GFSGI.IT..TGT.GSKL.GIVTS.D.DFLAEKD.TTLLSEVMTPRIELVVAPAGVTLKEA.EIL...S.
Retrocopy GFSGIRITR<TGTIGSKLLGIVTSQDTDFLAEKDTTTLLSEVMTPRIELVVAPAGVTLKEAKEIL<KCSE

Parental  KGKLPIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDV-IVLD
          KGKLPIVNDRDELVAII..TDLKKN.DYPLASKDS.KQLLC.AAVGTRED.KY.LDLL.QAGV...IVLD
Retrocopy KGKLPIVNDRDELVAIITHTDLKKN*DYPLASKDSHKQLLCRAAVGTREDEKYCLDLLSQAGVNI<IVLD

Parental  SSQ-GNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLI
          SSQ.GNS.YQI.MVHYIKQKYPHLQVIGGN.VTAAQAKNL.
Retrocopy SSQ<GNSAYQITMVHYIKQKYPHLQVIGGNMVTAAQAKNLM

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	0.83 RPM	16.92 RPM
SRP007412_cerebellum	1.09 RPM	9.12 RPM
SRP007412_heart	0.12 RPM	3.31 RPM
SRP007412_kidney	0.13 RPM	8.88 RPM
SRP007412_liver	0.09 RPM	5.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2346 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2346 has 0 orthologous retrocopies within eutheria group .

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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	ENSPPYG00000013884	1 retrocopy	retro_pabe_528,
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,