RetrogeneDB ID: retro_ggor_276

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:108683408..108685187(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MATR3
• Ensembl ID: ENSGGOG00000007308
• Aliases: None
• Description: None

Sequence

>retro_ggor_276
ATGTCCAAGTCATTCCAGCAGTCATCTCTCAGTAGGGACTAACAGGGTCATGGGTGTGACCTGTCTGCGGCAGGCATAGG
CCTTTCTGCTGCTGTTACCCAGTCTTTAAGTATGCCAGCATCTCTTAGGAAGGATGAACCAGGGTACTGCACGCCTTGCT
AGTTGAATGAATCTTGGAACGAATTCTTCATTGAATCAAAAAGGAGCTCATAGTGCACGGTCTTCTGCTAGTACTTCTTC
CCATAATTTACACTCTATATTTAACATTGGAAGTAGAGATCCACTCCCTTTATCTTCTCAACACTGTGGAGATGCAGACC
AGGCCAGTAACATTTTGGCCAGCTTTGGTTTGTCTGCTAGAGACTTAGATGAACTGAGTCATTATCCAGAGGACAAGATG
ACTCCTGAGAATTTGCCCCAAATCCTTCTACAGCTTAAAAGGAGGAGAACTGAAGAAGGCCCTACGTTGAATTATGGTAG
AGATGACAGATCTGCTGCATGGGAGCCACCATACAGAGTACCTAGGGATGATTCGGAAGAAAAAAAGGCACTTTAGAAGA
GATAGTTTTGATGATCATGGTCCTAGTCTCAACCTGGTGCTTGATTATGATCATGGAAGTCATTCTCGAGAATCTGGTTA
TTATGACAGAACGGATTATGAAGATAACAGATTACGAGATGGAAAAAAGTTGTAGGGATGATTCTTTTTTTGGTGAGACC
TCGCGTAACTATCATAAATTTGACAGTGAGTATGAAAGAATGGGACGCGGTCATGGTCCTGACCCTTTACAAGAGAGATC
TCTCTTTGAGAAAAAGAGGGGTGCTCCTCCAAGTAGCAATATTGAAGACTTTCATGGACTCTTACTGAAAGGTTATACCC
ATCTGTGCTCTATATGTGATTTGCCAGTTCATTCTAATGAGGAGTTGAGTCAACATATCAATAGAGCAAGCCACAGTCAT
CGATGCCAGCTTCTTCTTGAAATCTACCCAGAATGGGATCCTGACAATGATACAGAACACACAATGGGTGATCCATTCAT
GTCTCAGCAGTCTACAAACCCAGCACCAGGAATTCTGGGATCTCCACCTCCCTCGTTTCATCTTGGAGGACCAGCAATTG
GACCAAGAGGAAATCTGGGTGCTGGAAATGGAAACCTGCAAAGAACTAGACACATACAAAATGGCAGAGTGGAAACGAGC
AGAGTTGTTCACATCATGGATTTTCAGTGAGGGAAAAACTTGAGATACCAGCTATTACAGCTGGTAGAACCATTTGGAGT
CATTTCAAATCATCTGATTCTAAATAAAATTAATGAGGCATTTATTGAAAGGGCAACCACAGAGGATGCTCAGGCTGCAG
TGGATTATTATACAACCACACCAGTGTTAGTATTAGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAAAGAATA
AAGAAACCTGAAGGAAAGCCAGATCAGAAGTTTGATTGAAGGCAAGAGCTTGGATGTGTGATACATCGCAGCAATTTGCC
CCATTCTGCCTATTCTGATAGTGCTGTTCTCAAGCTTGCTGAGCCTTATGGGAAAATAAAGAATTACATATTAATGAGGA
TGAAAAGTCAGGCTTTTATTGAGATGGAGACAAGAGAAGATACAATGGCAATGGTTGACCATTGTTTGAAAAAAGCCCTT
TAGTTTCAGGGGAGATGTGTGAAGGTAGACCTGTCTAAGAAATATAAAAATCTAGTACTGAGGATTCCAAACAGAGGCAT
TGATTTACTGAAAAAAGAT

Alignment

ORF - retro_ggor_276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.58 %
• Parental protein coverage: 65.92 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSKSFQQSSLSRDSQGHGRDLSAAGIGLLAAATQSLSMPASL-GRMNQGTARLASLMNLGMSSSLNQQGA
          MSKSFQQSSLSRD.QGHG.DLSAAGIGL.AA.TQSLSMPASL.GRMNQGTARLAS.MNLG..SSLNQ.GA
Retrocopy MSKSFQQSSLSRD*QGHGCDLSAAGIGLSAAVTQSLSMPASL>GRMNQGTARLAS*MNLGTNSSLNQKGA

Parental  HSALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDADQASNILASFGLSARDLDELSRYPEDKITPENLP
          HSA.SSASTSSHNL.SIFNIGSR.PLPLSSQH.GDADQASNILASFGLSARDLDELS.YPEDK.TPENLP
Retrocopy HSARSSASTSSHNLHSIFNIGSRDPLPLSSQHCGDADQASNILASFGLSARDLDELSHYPEDKMTPENLP

Parental  QILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEK-RHFRRDSFDDRGPSLNPVLDYDHGSRS
          QILLQLKRRRTEEGPTL.YGRD.RSA..EPPYRVPRDD.EEK.RHFRRDSFDD.GPSLN.VLDYDHGS.S
Retrocopy QILLQLKRRRTEEGPTLNYGRDDRSAAWEPPYRVPRDDSEEK>RHFRRDSFDDHGPSLNLVLDYDHGSHS

Parental  QESGYYDRMDYEDDRLRDGER-CRDDSFFGETSHNYHKFDSEYERMGRG--PGPLQERSLFEKKRGAPPS
          .ESGYYDR.DYED.RLRDG...CRDDSFFGETS.NYHKFDSEYERMGRG..P.PLQERSLFEKKRGAPPS
Retrocopy RESGYYDRTDYEDNRLRDGKK>CRDDSFFGETSRNYHKFDSEYERMGRGHGPDPLQERSLFEKKRGAPPS

Parental  SNIEDFHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFML
          SNIEDFHGLL.KGY.HLCSICDLPVHSN.E.SQHIN.ASHS.RCQLLLEIYPEW.PDNDT.HTMGDPFM.
Retrocopy SNIEDFHGLLLKGYTHLCSICDLPVHSNEELSQHINRASHSHRCQLLLEIYPEWDPDNDTEHTMGDPFMS

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

Parental  LQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPD
          LQLVEPFGVISNHLILNKINEAFIE.ATTEDAQAAVDYYTTTP.LV.GKPVRVHLSQKYKRIKKPEGKPD
Retrocopy LQLVEPFGVISNHLILNKINEAFIERATTEDAQAAVDYYTTTPVLVLGKPVRVHLSQKYKRIKKPEGKPD

Parental  QKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKK
          QKFD..QELG.VIH.SNLPHS.YSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETRED.MAMVDHCLKK
Retrocopy QKFD*RQELGCVIHRSNLPHSAYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDTMAMVDHCLKK

Parental  ALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKD
          AL.FQGRCVKVDLS.KYK.LVLRIPNRGIDLLKKD
Retrocopy AL*FQGRCVKVDLSKKYKNLVLRIPNRGIDLLKKD

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	0.00 RPM	325.80 RPM
SRP007412_cerebellum	0.00 RPM	262.43 RPM
SRP007412_heart	0.00 RPM	33.30 RPM
SRP007412_kidney	0.00 RPM	178.81 RPM
SRP007412_liver	0.00 RPM	95.46 RPM
SRP007412_testis	0.00 RPM	380.21 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_276 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_276 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_199
Pan troglodytes	retro_ptro_181

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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,