RetrogeneDB ID: retro_hsap_1089

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:16553548..16555354(-)
• Located in intron of: ENSG00000008394

Retrocopy information

• Ensembl ID: ENSG00000256238
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUPT16H
• Ensembl ID: ENSG00000092201
• Aliases: SUPT16H, CDC68, FACTP140, SPT16/CDC68
• Description: suppressor of Ty 16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:11465]

Sequence

>retro_hsap_1089
ATGGCTGTGACTCTGGACAAAGACGCTTATTATCGGTGAGTGAAGAGACTGTACAGCAATTGGCAGAAAGGAGAAGATGA
GTATGCCAACGTTGAGCCATTGTTGCATCAGTGGGTGTTGATGAAGAAATTGTTTATTCCAAATCAACTGCCTTACAGAC
ATGGCTCTTTGGTTATGAACTAACTGATACTACCATGGTCTTTTGTGATGACAAAATCATCTTTATGGCCAGCAAAAAAA
AAGTGGAGTTTTTGAAACAAATTGCCAACACTAAGGGCAATGAGAATGCTAATGGAGCCCCTGCCATCAGACTGCTGATA
TGAGAAAAGAATGAAAGTAGTAAGAATAGCTTTGACAAAATGATTGAAGCCATTAAAGAAAGCAAGAATGGCAAGAAGAT
TGGAGTGTTCAGCAAAGACAAATTCCCTGGAGAGTTCATGAAGAGCTGGAATGACTGCCTCAACAAAGAAGGCTTTGACA
AAATAGATATCAGTGCAGTTGTGGCATATACAGTCGCTGTAAGGGAGGATGGGGAGCTCAAATTAATGAAGAAAGCAGCT
GGCATCACTTCTGAAGTCTTCAACAAATTCTTCAAGGAAAGAGTCATGGAAATAGTTGATGCAGATGAGAAAGTTTGACA
CAGCAAACTGGCTGAGTCTGTGGAAAAGGCCGTTGAAGAGAAAAAATACCTTGCTGGGGCAGACCCTTCTACTGTGGAAA
TGTGTTACCCTCCTATCATTCAGAGTGGTGGCAACTATAATCTCAAGTTCAGTGTGGTGAGTGACAAGAATCACATGTAT
TTTGGGGCTATCACTTGTGCCATGGGTATTCGCTTCGAGTCTTATTGCTCCAACCTGTTCGCACTTTGATGGCTGATCCT
CCTCAGGAAGTTCAAGAAAATTACAACTTTTTACTCCAGCTTCAAGAAGAGCTGCTGAAGGAATTAAGACATGGTGTGAA
GATATGTGATGTATATAATGCTGTCATGGACGTGGCTAAAAAGCAGAAGCCAGAACTCCTGAACAAAATTACCAGAAACC
TAGGATTTGGGGTGGGAATTGAATTCCATGAAAGCTTCCTAGTAATCAATAGTAAAAATCAATACAAACTGAAGACAGGA
ATGGTTTTCAGCATCAGTTTGGGATTCTCAGACCTGACTAACAAGGAGGGGAAAAAGCCAGAAGAGAAAACCTATGCCCT
GTTCCTTAGTGACACAGTGCTTATGGATGAGGATGGCCCAGCTACTGTTCTCACTTCTGTGAAGAAGAAAGTGAAGAATG
TGGGTATTTTCCTAAGGAACGAAGATGAGGAAAAGGAGGAGGAGGAGAAAGATGAGGCAGAGGACCTTTTGGGAAGAGGT
TCTCGGGCAGCATTACTTACAGAAAGAACAGGAATGAAATGACTGCAGAAGAGAAGTGAAGAGCACATCAAAAAGAACTA
GTGGCTCAACTCAATGAAGAAGCAAAGAGGTGACTGACTGAACAAAAGGGAGAACAGGAGATTCAGAAAGCTCACAAATC
TAATGTGTCCTATAAACACCCATCTCTGATGCCTAAGGAACCACATATTGGGGAAATGAAGATCTACATCGATAAGAAAT
ATGAGACTGTAATAATGCCTGTGTTTGGCATTGCAACACCTTTTCACATTGCCACAATCAAGAATATAAGTATGTCCGTG
GAAGGAGATTATACTTACTTGCAAATCAACTTTTATTGCCCAGGCAGTGCTCTGGGCAGGAATGAAGGCAACATCTTTCC
TAACCCTGAAGCGACTTTTGTCAAAGAAATTACATACCAAGCGTCA

Alignment

ORF - retro_hsap_1089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.08 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAVTLDKDAYYRRVKRLYSNWRKGEDEYANVD-AIVVSVGVDEEIVYAKSTALQTWLFGYELTDTIMVFC
          MAVTLDKDAYYR.VKRLYSNW.KGEDEYANV..AIV.SVGVDEEIVY.KSTALQTWLFGYELTDT.MVFC
Retrocopy MAVTLDKDAYYR*VKRLYSNWQKGEDEYANVE<AIVASVGVDEEIVYSKSTALQTWLFGYELTDTTMVFC

Parental  DDKIIFMASKKKVEFLKQIANTKGNENANGAPAITLLIREKNESNKSSFDKMIEAIKESKNGKKIGVFSK
          DDKIIFMAS...VEFLKQIANTKGNENANGAPAI.LLI.EKNES.K.SFDKMIEAIKESKNGKKIGVFSK
Retrocopy DDKIIFMASXXXVEFLKQIANTKGNENANGAPAIRLLI*EKNESSKNSFDKMIEAIKESKNGKKIGVFSK

Parental  DKFPGEFMKSWNDCLNKEGFDKIDISAVVAYTIAVKEDGELNLMKKAASITSEVFNKFFKERVMEIVDAD
          DKFPGEFMKSWNDCLNKEGFDKIDISAVVAYT.AV.EDGEL.LMKKAA.ITSEVFNKFFKERVMEIVDAD
Retrocopy DKFPGEFMKSWNDCLNKEGFDKIDISAVVAYTVAVREDGELKLMKKAAGITSEVFNKFFKERVMEIVDAD

Parental  EKVRHSKLAESVEKAIEEKKYLAGADPSTVEMCYPPIIQSGGNYNLKFSVVSDKNHMHFGAITCAMGIRF
          EKV.HSKLAESVEKA.EEKKYLAGADPSTVEMCYPPIIQSGGNYNLKFSVVSDKNHM.FGAITCAMGIRF
Retrocopy EKV*HSKLAESVEKAVEEKKYLAGADPSTVEMCYPPIIQSGGNYNLKFSVVSDKNHMYFGAITCAMGIRF

Parental  KSYCSNL-VRTLMVDPSQEVQENYNFLLQLQEELLKELRHGVKICDVYNAVMDVVKKQKPELLNKITKNL
          .SYCSNL.VRTLM.DP.QEVQENYNFLLQLQEELLKELRHGVKICDVYNAVMDV.KKQKPELLNKIT.NL
Retrocopy ESYCSNL<VRTLMADPPQEVQENYNFLLQLQEELLKELRHGVKICDVYNAVMDVAKKQKPELLNKITRNL

Parental  GFGMGIEFREGSLVINSKNQYKLKKGMVFSINLGFSDLTNKEGKKPEEKTYALFIGDTVLVDEDGPATVL
          GFG.GIEF.E..LVINSKNQYKLK.GMVFSI.LGFSDLTNKEGKKPEEKTYALF..DTVL.DEDGPATVL
Retrocopy GFGVGIEFHESFLVINSKNQYKLKTGMVFSISLGFSDLTNKEGKKPEEKTYALFLSDTVLMDEDGPATVL

Parental  TSVKKKVKNVGIFLKNEDEEEEEEEKDEAEDLLGRGSRAALLTERT-RNEMTAEEKRRAHQKELAAQLNE
          TSVKKKVKNVGIFL.NEDEE.EEEEKDEAEDLLGRGSRAALLTERT.RNEMTAEEK.RAHQKEL.AQLNE
Retrocopy TSVKKKVKNVGIFLRNEDEEKEEEEKDEAEDLLGRGSRAALLTERT<RNEMTAEEK*RAHQKELVAQLNE

Parental  EAKRRLTEQKGEQQIQKARKSNVSYKNPSLMPKEPHIREMKIYIDKKYETVIMPVFGIATPFHIATIKNI
          EAKR.LTEQKGEQ.IQKA.KSNVSYK.PSLMPKEPHI.EMKIYIDKKYETVIMPVFGIATPFHIATIKNI
Retrocopy EAKR*LTEQKGEQEIQKAHKSNVSYKHPSLMPKEPHIGEMKIYIDKKYETVIMPVFGIATPFHIATIKNI

Parental  SMSVEGDYTYLRINFYCPGSALGRNEGNIFPNPEATFVKEITYRAS
          SMSVEGDYTYL.INFYCPGSALGRNEGNIFPNPEATFVKEITY.AS
Retrocopy SMSVEGDYTYLQINFYCPGSALGRNEGNIFPNPEATFVKEITYQAS

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	0.38 RPM	124.04 RPM
bodymap2_adrenal	0.16 RPM	131.86 RPM
bodymap2_brain	0.02 RPM	129.25 RPM
bodymap2_breast	0.29 RPM	93.78 RPM
bodymap2_colon	0.14 RPM	129.86 RPM
bodymap2_heart	0.04 RPM	45.01 RPM
bodymap2_kidney	0.14 RPM	86.69 RPM
bodymap2_liver	0.02 RPM	34.14 RPM
bodymap2_lung	0.00 RPM	61.30 RPM
bodymap2_lymph_node	0.00 RPM	89.78 RPM
bodymap2_ovary	0.13 RPM	203.27 RPM
bodymap2_prostate	0.00 RPM	137.40 RPM
bodymap2_skeletal_muscle	0.02 RPM	63.22 RPM
bodymap2_testis	0.36 RPM	211.81 RPM
bodymap2_thyroid	0.02 RPM	163.76 RPM
bodymap2_white_blood_cells	0.08 RPM	173.65 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1089 was not detected

EST

No EST(s) were mapped for retro_hsap_1089 retrocopy.

TSS

No TSS is located nearby retro_hsap_1089 retrocopy 5' end.

Lab

retro_hsap_1089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1089 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_741
Gorilla gorilla	retro_ggor_857

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000092201	1 retrocopy	retro_hsap_1089 ,
Gorilla gorilla	ENSGGOG00000002243	1 retrocopy	retro_ggor_857,
Nomascus leucogenys	ENSNLEG00000014392	1 retrocopy	retro_nleu_1624,
Pan troglodytes	ENSPTRG00000006122	1 retrocopy	retro_ptro_741,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.14 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.09 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.14 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.06 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.07 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.14 RPM
TSI_NA20786	0.16 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.08 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.14 RPM

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Indel association:

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