RetrogeneDB ID: retro_hsap_3011

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:176415764..176417153(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000251174
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSEN2
• Ensembl ID: ENSG00000154743
• Aliases: TSEN2, PCH2B, SEN2, SEN2L
• Description: tRNA splicing endonuclease 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28422]

Sequence

>retro_hsap_3011
ATGGCAGAAGCAGTTTTCCATGCCCCAAACAGGAAAGGAAGAGTGTATGAGACTTATGAGTCTCCATTGCCAATCCCTTC
TGGTCAGGACCATGGTCCTCAGAAAGCAAGATATTCAATGCTGGAATGATTAACAACAATGTGATTGTGAGGAATGCAGA
GGACATTGAGCCGCTCTATGGGGAAGGTTCTTTTGGAAAAGGTATTCTTTCAAGAAACTGTCCAACCATCACAGTTTCAG
ATCCTAAATTGGTTGCTAAATGGAAAGATATGAAGACAAACATGCCTATCATCACGTCAAAGAAGTATCAGCGTAGTGTT
GAGTGGGTGGCAGAGCGGATGCGTAGACAGGGACAGGATGAGAGTGCGGTGCGCAGAATCCTCAAGGATTACTTGAATCC
GCTTGAGCATCGCCCTGTGAAAAGGAATGAACAGGTTCAAATGCATGATGAGCTTAACTCTGGAATGGTCTCCAACATGG
AAGGCACAGCGGTAGGAGAGAGACCTTCTATGATAAACGGGGACTCTGGAAAGTCAGTTGTTATGGGTGATCCCAGTGAG
CCATTAGGCTGCCTGCAGGAGGGCTCTGGGAGCGACCCACCAACAGAAGGCTTTGAGGAAAGCGTGGGAGAGGACGCTTC
ACCTCTGCCCCCAGCATGTTACTCCAAACACGATGCTCTCGTCCTCCAGTCTGGCCCTCACCGTGAGGACAGCAGCCAGC
ATTTTGGTCTCCTGCATGCTGGGGACAGAGGGCCTGACCAGTACGTGCTGGTGCAGGAAGCCAAGTGTGCCGTGAGCGAG
AGGAAGGATGCCCCAAATGAGGAATTGGTGCAAAGAAAGAGACTAATCTGCAGAAGAAATCCATATAGGATCTTTTGAGT
ATTTGCAGCTCAGCCTAGAAGAGGTCTTCTTCCTGGTCTATGCTCTGGAATGTTTTAAGTATTTGCTATGAGAAGGAGCC
TTTAACGATAGCGAAGCTCTGGAAAGCTTTCACCGTAGTTCAGCTTACGTTCAGGACCACCTCCATGGTCTACCATTGCT
TGCCAAGCAATGGCTAGTGCCCAAAGTGGGGCTCAAGTACGGGACAGATTTACTGTTATATTGGAAAGGCCCTCCGTTTT
ACCATGCAAGCTATTCTGTCGTTATTGAGCTAGTTGATGAGCAGTTTGAAGGCTGTCTCTGCAGGCCTTTCAGTTGGATG
TCCCTGGCTGCCTTGAGCAGAGTTTCCGTTAATGTCTCCAAGGAACTCATGCTGTGCTGTTTCATTAAACCCGCTACTAT
GACTGACAAGGAAATGGAGTCACCAGAATGTATGAAAAAAATTAGAGTTCAGGAGGTGATTCTGAGTTGATGGGTGTCTT
CACAAGAGAGGAGTGACCAAGACAAACTT

Alignment

ORF - retro_hsap_3011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAEAVFHAPKRKRRVYETYESPLPIPFGQDH-GPLK-EFKIFRAEMINNNVIVRNAEDIEQLYGKGYFGK
          MAEAVFHAP.RK.RVYETYES..P.P......GP...E.KIF.A.MINNNVIVRNAEDIE.LYG.G.FGK
Retrocopy MAEAVFHAPNRKGRVYETYES--PLPIPSGQ<GPWSSESKIFNAGMINNNVIVRNAEDIEPLYGEGSFGK

Parental  GILSRSRPSFTISDPKLVAKWKDMKTNMPIITSKRYQHSVEWAAELMRRQGQDESTVRRILKDYTKPLEH
          GILSR..P..T.SDPKLVAKWKDMKTNMPIITSK.YQ.SVEW.AE.MRRQGQDES.VRRILKDY..PLEH
Retrocopy GILSRNCPTITVSDPKLVAKWKDMKTNMPIITSKKYQRSVEWVAERMRRQGQDESAVRRILKDYLNPLEH

Parental  PPVKRNEEAQVHDKLNSGMVSNMEGTAGGERPSVVNGDSGKSGGVGDPREPLGCLQEGSGCHPTTESFEK
          .PVKRNE..Q.HD.LNSGMVSNMEGTA.GERPS..NGDSGKS...GDP.EPLGCLQEGSG..P.TE.FE.
Retrocopy RPVKRNEQVQMHDELNSGMVSNMEGTAVGERPSMINGDSGKSVVMGDPSEPLGCLQEGSGSDPPTEGFEE

Parental  SVREDASPLPHVCCCKQDALILQRGLHHEDGSQHIGLLHPGDRGPDHEYVLVEEAECAMSEREAAPNEEL
          SV.EDASPLP..C..K.DAL.LQ.G.H.ED.SQH.GLLH.GDRGPD..YVLV.EA.CA.SER..APNEEL
Retrocopy SVGEDASPLPPACYSKHDALVLQSGPHREDSSQHFGLLHAGDRGPD-QYVLVQEAKCAVSERKDAPNEEL

Parental  VQRNRLICRRNPYRI-FEYLQLSLEEAFFLVYALGC-LSIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAY
          VQR.RLICRRNPYRI.FEYLQLSLEE.FFLVYAL.C.LSI.YEKEPLTI.KLWKAFTVVQ.TFRTT.M.Y
Retrocopy VQRKRLICRRNPYRI>FEYLQLSLEEVFFLVYALEC>LSICYEKEPLTIAKLWKAFTVVQLTFRTTSMVY

Parental  HYFRSKG-WVPKVGLKYGTDLLLYRKGPPFYHASYSVIIELVDDHFEGSLRRPLSWKSLAALSRVSVNVS
          H...S.G..VPKVGLKYGTDLLLY.KGPPFYHASYSV.IELVD..FEG.L.RP.SW.SLAALSRVSVNVS
Retrocopy HCLPSNG<LVPKVGLKYGTDLLLYWKGPPFYHASYSVVIELVDEQFEGCLCRPFSWMSLAALSRVSVNVS

Parental  KELMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSRWVSSRERSDQDDL
          KELMLC..IKP.TMTDKEMESPECMK.I.VQEVILS.WVSS.ERSDQD.L
Retrocopy KELMLCCFIKPATMTDKEMESPECMKKIRVQEVILS*WVSSQERSDQDKL

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	0.00 RPM	4.85 RPM
bodymap2_adrenal	0.00 RPM	16.09 RPM
bodymap2_brain	0.00 RPM	8.81 RPM
bodymap2_breast	0.00 RPM	7.26 RPM
bodymap2_colon	0.00 RPM	7.58 RPM
bodymap2_heart	0.00 RPM	6.78 RPM
bodymap2_kidney	0.00 RPM	7.98 RPM
bodymap2_liver	0.00 RPM	3.27 RPM
bodymap2_lung	0.00 RPM	2.18 RPM
bodymap2_lymph_node	0.00 RPM	3.93 RPM
bodymap2_ovary	0.00 RPM	13.17 RPM
bodymap2_prostate	0.02 RPM	12.47 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.17 RPM
bodymap2_testis	0.04 RPM	10.43 RPM
bodymap2_thyroid	0.00 RPM	11.64 RPM
bodymap2_white_blood_cells	0.00 RPM	3.90 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3011 was not detected

EST

No EST(s) were mapped for retro_hsap_3011 retrocopy.

TSS

No TSS is located nearby retro_hsap_3011 retrocopy 5' end.

Lab

retro_hsap_3011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3011 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2035
Gorilla gorilla	retro_ggor_2085
Pongo abelii	retro_pabe_2495
Macaca mulatta	retro_mmul_1925

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000154743	1 retrocopy	retro_hsap_3011 ,
Gorilla gorilla	ENSGGOG00000012488	2 retrocopies	retro_ggor_1826, retro_ggor_2085,
Microcebus murinus	ENSMICG00000016672	1 retrocopy	retro_mmur_883,
Macaca mulatta	ENSMMUG00000007195	1 retrocopy	retro_mmul_1925,
Pongo abelii	ENSPPYG00000013647	1 retrocopy	retro_pabe_2495,
Pan troglodytes	ENSPTRG00000014633	1 retrocopy	retro_ptro_2035,

Population studies

Expression level across human populations :

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

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Indel association:

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