RetrogeneDB ID: retro_hsap_2368

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:202002798..202003719(-)
• Located in intron of: ENSG00000003402

Retrocopy information

• Ensembl ID: ENSG00000232133
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSG00000106348
• Aliases: IMPDH1, IMPD, IMPD1, LCA11, RP10, sWSS2608
• Description: IMP (inosine 5'-monophosphate) dehydrogenase 1 [Source:HGNC Symbol;Acc:6052]

Sequence

>retro_hsap_2368
CAGCAGCTCTTCGCCAGTGACCAGGGACTCACCTACAACGACTTCTTGATTCTCCCAGGATTCATAGACTTCATAGCTGA
TGAGGTGGACCTGACCTCAGCCCTGACCCAATGGTCACTCTGAAGACGCCGCTGATCTCCTCCCCCATGGACACTGTGAC
AGAGGCCGACCTGGCCATCGTGATGGCTCTGATGGGAGGTACTGGTTTCATTCACCACAACTGCACCCCAGAGTTCCAGG
CCAGTGAGGTGCAGAAGGTCAAGAAGTTTGAACCGGGCTTTATCACACACCCCGTGGTGCTGAGCCCCTTGCACACTGTG
GGTGATGTGTTGGAGGCCAAGATGCGTCATGGCTTCTCTGGCATCCCCATCACTGAGACGGGTACCATGGGCAGCAAGCT
GGTGGGCATCGTCACCTCCCGAGACATCGACTTTCTTGCTGAGAAGGACCACACCACCCTCCTCAGTGAGGTGATGATGC
CAAGGATCAAGCTAGTGGTGGCTCCAGCAGTGTGAGGTTGAAAGAGGCAAATGAGATCCTGCAGCTTAGTAAGAAAGGAA
GCTGCCTATCGTCAATGATCGCGATGAGCTGGTGGCCATTATCACCTGCACCGCGCTGAAGAACCGAGACTACCCTGTGG
CCTCCAAGGATTCCCATGAGCAGCTGCTGGGCGGGGCAGCTGTGGGTACCCATGAGGATGACAAATACCACCTGGACCTG
CTCACCCAGGTAGGCGTCAATGTCATAGGCTTGGACTCGTCCCAAGGGAACTCGGTGTATCAGATCGCCATGGTGCATTA
CATCAAACAAAAGTAACCCCACCTCCAGGTGATTGGGGGGAACGTGGTGACAGCAGCCCAGGCCAACAACCTGATTGACG
CTGGTGTGGATGGGCTGGGCAGGGGCATGGACTGCGCGGCT

Alignment

ORF - retro_hsap_2368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 52.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTR-KITLKTPLISSPMDTVTEADMAIAMALMGGIG
          QQLFAS..GLTYNDFLILPGFIDFIADEVDLTSALT....TLKTPLISSPMDTVTEAD.AI.MALMGG.G
Retrocopy QQLFASDQGLTYNDFLILPGFIDFIADEVDLTSALTQ<MVTLKTPLISSPMDTVTEADLAIVMALMGGTG

Parental  FIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIVT
          FIHHNCTPEFQA.EV.KVKKFE.GFIT.PVVLSP.HTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIVT
Retrocopy FIHHNCTPEFQASEVQKVKKFEPGFITHPVVLSPLHTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIVT

Parental  SRDIDFLAEKDHTTLLSEVMTPRIELVVAPA-GVTLKEANEILQRSKKG-KLPIVNDCDELVAIIARTDL
          SRDIDFLAEKDHTTLLSEVM.PRI.LVVAPA..V.LKEANEILQ.SKKG.KLPIVND.DELVAII..T.L
Retrocopy SRDIDFLAEKDHTTLLSEVMMPRIKLVVAPA<SVRLKEANEILQLSKKG<KLPIVNDRDELVAIITCTAL

Parental  KKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIKQKYPHL
          .KNRDYP.ASKDS..QLL.GAAVGT.EDDKY.LDLLTQ.GV.VI.LDSSQGNSVYQIAMVHYIKQK.PHL
Retrocopy -KNRDYPVASKDSHEQLLGGAAVGTHEDDKYHLDLLTQVGVNVIGLDSSQGNSVYQIAMVHYIKQK*PHL

Parental  QVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGS
          QVIGGNVVTAAQA.NLIDAGVDGL..GM.C..
Retrocopy QVIGGNVVTAAQANNLIDAGVDGLGRGMDCAA

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
bodymap2_adipose	4.00 RPM	54.51 RPM
bodymap2_adrenal	9.78 RPM	33.80 RPM
bodymap2_brain	0.73 RPM	6.45 RPM
bodymap2_breast	5.08 RPM	24.55 RPM
bodymap2_colon	2.03 RPM	23.28 RPM
bodymap2_heart	1.99 RPM	11.10 RPM
bodymap2_kidney	2.25 RPM	12.92 RPM
bodymap2_liver	1.01 RPM	2.60 RPM
bodymap2_lung	12.87 RPM	18.14 RPM
bodymap2_lymph_node	9.65 RPM	42.47 RPM
bodymap2_ovary	0.64 RPM	24.71 RPM
bodymap2_prostate	1.30 RPM	22.01 RPM
bodymap2_skeletal_muscle	0.69 RPM	1.29 RPM
bodymap2_testis	0.92 RPM	17.72 RPM
bodymap2_thyroid	3.77 RPM	8.32 RPM
bodymap2_white_blood_cells	7.25 RPM	90.88 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2368 was not detected

EST

1 EST(s) were mapped to retro_hsap_2368 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF081886	202002868	202003132	99.3	258	2	252

TSS

No TSS is located nearby retro_hsap_2368 retrocopy 5' end.

Lab

retro_hsap_2368 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2368 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1798
Pongo abelii	retro_pabe_2138

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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,
Homo sapiens	ENSG00000178035	1 retrocopy	retro_hsap_697,
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	ENSPTRG00000019660	7 retrocopies	retro_ptro_1087, retro_ptro_1724, retro_ptro_1758, retro_ptro_2575, retro_ptro_2719, retro_ptro_2886, retro_ptro_3198,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	6.40 RPM
CEU_NA11843	4.27 RPM
CEU_NA11930	8.31 RPM
CEU_NA12004	7.48 RPM
CEU_NA12400	4.77 RPM
CEU_NA12751	16.37 RPM
CEU_NA12760	10.60 RPM
CEU_NA12827	5.75 RPM
CEU_NA12872	10.10 RPM
CEU_NA12873	9.28 RPM
FIN_HG00183	9.01 RPM
FIN_HG00277	8.50 RPM
FIN_HG00315	7.89 RPM
FIN_HG00321	7.50 RPM
FIN_HG00328	7.27 RPM
FIN_HG00338	6.56 RPM
FIN_HG00349	8.62 RPM
FIN_HG00375	8.73 RPM
FIN_HG00377	8.55 RPM
FIN_HG00378	12.11 RPM
GBR_HG00099	5.55 RPM
GBR_HG00111	4.26 RPM
GBR_HG00114	6.73 RPM
GBR_HG00119	9.70 RPM
GBR_HG00131	6.21 RPM
GBR_HG00133	8.10 RPM
GBR_HG00134	7.08 RPM
GBR_HG00137	8.27 RPM
GBR_HG00142	9.28 RPM
GBR_HG00143	5.42 RPM
TSI_NA20512	4.61 RPM
TSI_NA20513	4.72 RPM
TSI_NA20518	8.24 RPM
TSI_NA20532	11.29 RPM
TSI_NA20538	12.12 RPM
TSI_NA20756	6.14 RPM
TSI_NA20765	7.46 RPM
TSI_NA20771	10.75 RPM
TSI_NA20786	7.40 RPM
TSI_NA20798	5.92 RPM
YRI_NA18870	5.82 RPM
YRI_NA18907	7.14 RPM
YRI_NA18916	7.43 RPM
YRI_NA19093	10.57 RPM
YRI_NA19099	5.75 RPM
YRI_NA19114	5.56 RPM
YRI_NA19118	8.10 RPM
YRI_NA19213	9.35 RPM
YRI_NA19214	7.97 RPM
YRI_NA19223	5.11 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).