RetrogeneDB ID: retro_hsap_199

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:106434360..106436139(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232952
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MATR3
• Ensembl ID: ENSG00000015479
• Aliases: MATR3, MPD2, VCPDM
• Description: matrin 3 [Source:HGNC Symbol;Acc:6912]

Sequence

>retro_hsap_199
GTGTCCAAGTCATTCCAGCAGTCATCTCCCAGTAGGGACTAACAGGGTCATGGGTGTGACCTGTCTGCGGCAGGCATAGG
CCTTCCTGCTGCTGTTACCCAGTCTTTAAGTATGCCAGCATCTCTTAGGAAGGATGAACCAGGGTACTGCACGCCTTGCT
AGTTGAATGAATCTTGGAACGAATTCTTCATTGAATCAAAAAGGAGCTCATAGTGCACGGTCTTCTGCTAGTACTTCTTC
CTATAATTTACAGTCTATATTTAACATTGGAAGTAGAGGTCCACTCCCTTTATCTTCTCAACACTGTGGAGATGCAGACC
AGGCCAGTAACATTTTGGCCAGCTTTGGTCTGTCTCCTAGAGACTTAGATGAACTGAGTCGTTATCCAGAGGACAAGATG
ACTCCTGAGAATTTTCCCCAAATCCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACTTTGAGTAATGGTAG
AGATGACAGATCTGCTGCATAGGAGCCACCATACAGAGTACCTAGGGATGATTCAGAAGAAAAAAAGGCACTTTAGAAGA
GATAGTTTTGATGATCATGGTCCTAGTCTCAACCTGGTGCTTGATTATGATCATGGAAGTCATTCTCGAGAATCTGGCTA
TTATGACAGAATGGATTATGAAGATGACAGATTACGAGATGGAAAAAAGGTGTAGGGATGATTCTTTTTTTGGTGAGACC
TCGCGTAACTATCATAAATTTGACAGTGAGTATGAAAGAATGGGACTTGGTCATGGTCCTGACCCTTTACAAGAGAGATC
TCTCTTTGAGAAAAAGAGGGGCGCTCCTCCAAGCAGCAATATTGAAGACTTTCATGGACTCTTACTGAAAGGTTATACCC
ATCTGTGCTCTATATGTGATTTGCCAGTTCATTCTAATGAGGAGTTGAGTCAACATATCAATAGAGCAAGCCACAGTCGT
CGATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGGATCCTGACAATGATACAAAACACACAATGGGTGATCCATTCAT
GTCTCAGCAGTCTACAAACCCAGCACCAGGAATTCTGGGATCTCCACCTCCCTCGTTTCATCTTGGAGGACCAGCAATTG
GACCAAGAGGAAATCTGGGTGCTGGAAATGGAAACCTGCAAAGAACTAGACACATACAAAATGGCAGAGTGGAAACGAGC
AGAGTTGTTCACATCATGGATTTTCAGTGAGGGAAAAACTTGAGATACCAGCTATTACAGCTGGTAGAACCATTTGGAGT
CATTTCAAATCATCTGATTCTAAATAAAATTAATGAGGCATTTATTGAAAGGGCAACCACAGAGGATGCTCAGGCTGCAG
TGGATTATTATACAACCACACCAGCATTAGTATTAGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAAAGAATA
AAGAAACCTGAAGGAAAGCCAGATCAGAAGTTTGATCGAAGGCAAGAGCTTGGATGTGTGATACATCGCAGCAATTTGCC
CCATTCTGCCTATTCTGATAGTGCTGTTCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTACATATTGATGAGGA
TGAAAAGTCAGGCTTTTATTGAGATGGAGACAAGAGAAGATGCAATGGCAATGGTTGACCATTGTTTGAAAAAAGCCCTT
TAGTTTCAGGGGAGATGTGTGAAGGTAGACCTGTCTGAGAAATATAAAAATCTAGTACTGAGGATTCCAAACAGAGGCAT
TGATTTACTGAAAAAAGAT

Alignment

ORF - retro_hsap_199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.25 %
• Parental protein coverage: 69.66 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSKSFQQSSLSRDSQGHGRDLSAAGIGLLAAATQSLSMPASL-GRMNQGTARLASLMNLGMSSSLNQQGA
          .SKSFQQSS.SRD.QGHG.DLSAAGIGL.AA.TQSLSMPASL.GRMNQGTARLAS.MNLG..SSLNQ.GA
Retrocopy VSKSFQQSSPSRD*QGHGCDLSAAGIGLPAAVTQSLSMPASL>GRMNQGTARLAS*MNLGTNSSLNQKGA

Parental  HSALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDADQASNILASFGLSARDLDELSRYPEDKITPENLP
          HSA.SSASTSS.NLQSIFNIGSRGPLPLSSQH.GDADQASNILASFGLS.RDLDELSRYPEDK.TPEN.P
Retrocopy HSARSSASTSSYNLQSIFNIGSRGPLPLSSQHCGDADQASNILASFGLSPRDLDELSRYPEDKMTPENFP

Parental  QILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEK-RHFRRDSFDDRGPSLNPVLDYDHGSRS
          QILLQLKRRRTEEGPTLS.GRD.RSA..EPPYRVPRDD.EEK.RHFRRDSFDD.GPSLN.VLDYDHGS.S
Retrocopy QILLQLKRRRTEEGPTLSNGRDDRSAA*EPPYRVPRDDSEEK>RHFRRDSFDDHGPSLNLVLDYDHGSHS

Parental  QESGYYDRMDYEDDRLRDGE-RCRDDSFFGETSHNYHKFDSEYERMG--RGPGPLQERSLFEKKRGAPPS
          .ESGYYDRMDYEDDRLRDG..RCRDDSFFGETS.NYHKFDSEYERMG...GP.PLQERSLFEKKRGAPPS
Retrocopy RESGYYDRMDYEDDRLRDGK>RCRDDSFFGETSRNYHKFDSEYERMGLGHGPDPLQERSLFEKKRGAPPS

Parental  SNIEDFHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFML
          SNIEDFHGLL.KGY.HLCSICDLPVHSN.E.SQHIN.ASHSRRCQLLLEIYPEW.PDNDT.HTMGDPFM.
Retrocopy SNIEDFHGLLLKGYTHLCSICDLPVHSNEELSQHINRASHSRRCQLLLEIYPEWDPDNDTKHTMGDPFMS

Parental  QQSTNPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQL
          QQSTNPAPGILG.PPPSFHLGGPA.GPRGNLGAGNGNLQ..RH.Q.GRVETSRVVHIMDFQ.GKNLRYQL
Retrocopy QQSTNPAPGILGSPPPSFHLGGPAIGPRGNLGAGNGNLQRTRHIQNGRVETSRVVHIMDFQ*GKNLRYQL

Parental  LQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPD
          LQLVEPFGVISNHLILNKINEAFIE.ATTEDAQAAVDYYTTTPALV.GKPVRVHLSQKYKRIKKPEGKPD
Retrocopy LQLVEPFGVISNHLILNKINEAFIERATTEDAQAAVDYYTTTPALVLGKPVRVHLSQKYKRIKKPEGKPD

Parental  QKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKK
          QKFD..QELG.VIH.SNLPHS.YSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKK
Retrocopy QKFDRRQELGCVIHRSNLPHSAYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKK

Parental  ALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKD
          AL.FQGRCVKVDLSEKYK.LVLRIPNRGIDLLKKD
Retrocopy AL*FQGRCVKVDLSEKYKNLVLRIPNRGIDLLKKD

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	0.04 RPM	250.26 RPM
bodymap2_adrenal	0.00 RPM	346.81 RPM
bodymap2_brain	0.05 RPM	686.49 RPM
bodymap2_breast	0.02 RPM	240.31 RPM
bodymap2_colon	0.00 RPM	347.81 RPM
bodymap2_heart	0.04 RPM	217.05 RPM
bodymap2_kidney	0.02 RPM	354.61 RPM
bodymap2_liver	0.02 RPM	85.89 RPM
bodymap2_lung	0.02 RPM	286.78 RPM
bodymap2_lymph_node	0.02 RPM	374.19 RPM
bodymap2_ovary	0.15 RPM	587.39 RPM
bodymap2_prostate	0.03 RPM	383.61 RPM
bodymap2_skeletal_muscle	0.05 RPM	267.73 RPM
bodymap2_testis	0.00 RPM	479.92 RPM
bodymap2_thyroid	0.00 RPM	534.58 RPM
bodymap2_white_blood_cells	0.02 RPM	403.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_199 was not detected

EST

No EST(s) were mapped for retro_hsap_199 retrocopy.

TSS

No TSS is located nearby retro_hsap_199 retrocopy 5' end.

Lab

retro_hsap_199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_199 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_181
Gorilla gorilla	retro_ggor_276

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006888	1 retrocopy	retro_cjac_3950,
Homo sapiens	ENSG00000015479	1 retrocopy	retro_hsap_199 ,
Gorilla gorilla	ENSGGOG00000007308	2 retrocopies	retro_ggor_276, retro_ggor_421,
Nomascus leucogenys	ENSNLEG00000009093	1 retrocopy	retro_nleu_1849,
Oryctolagus cuniculus	ENSOCUG00000026311	1 retrocopy	retro_ocun_652,
Otolemur garnettii	ENSOGAG00000010607	1 retrocopy	retro_ogar_3417,
Pongo abelii	ENSPPYG00000015835	2 retrocopies	retro_pabe_1722, retro_pabe_438,
Pan troglodytes	ENSPTRG00000017294	1 retrocopy	retro_ptro_181,
Rattus norvegicus	ENSRNOG00000019875	2 retrocopies	retro_rnor_1124, retro_rnor_475,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.09 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.03 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.19 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.14 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.02 RPM

---

Indel association:

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