RetrogeneDB ID: retro_ggor_2505

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:18088194..18089149(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNMTL1
• Ensembl ID: ENSGGOG00000015518
• Aliases: None
• Description: None

Sequence

>retro_ggor_2505
AGAACCTGCAGTGTAATGACACTAGTTAAGTCCAGGCCTTTTCGGGAAAAGCAAGGGAAGATACTGCTGAAAGGTCGCAG
GCTCATTGCAGACGATCTCAAGGCTGGAGCTGTGCTGAAAGTTTTCTTCTCTAGCCATCTATAATACATAAAGAAGCTGC
TCATCGATAAGCTGAAGGGTGTCAGCCTCATTAAGATGAAATTCGAGGACATCAAGGGTTGGTCCAACCTAGTAATGCCA
CAAGAATAATGGGGATTTTTGCCAAACCTGACCATGTTAACATGACATATCCAAAGACTCAGCTTTAGCACTCACTGCCT
TTATTATTGATTTGTGACAGTCTCTGCGACCCTGGGAACCTGGGGACAATTCTGAGATCTCCAGCTGGGGAAGGCTGCAG
CAAAGTGTTACTCACTTTGAAAGGCTGTGTGGATGCCTGGGAGCCCAAAGTGCTACAGGCGGCTATGGGTGCACATTTCC
AAGTGCCCATTATCAATAATCTGAAAACGAAACAGTGCCAAATTACCTGCTCCCTGACACCCAGGTCTGTGTGGCTGACA
ACTGAAGCCTTTATGCTCAGGCTCAGATGTCTAATAAAGCCAGGGACTATGGCTGGGTGTAGGATTGGCGATTCCTGAAG
TTTCACAAGTATGAAGAAAAGCAAGGTCTAGAAACTGGAGCCAGTAAAGGTTTGCTGCCTGTTATTGAGGTTCAGAGTTA
TGACTTGGACTGGACAGAGGCACCAGCAGCTGTAGTGGTTGGTGGCGAGACCTACGGCATGATCCTGGAATCTCTGTAGT
TGGCCGAGAGCCCTGCGGGCAAGAGGCTGCTGATCCCTGTTGCACCTGGAGTGGACAGCCTCAACTCGGCCATGGCTGCA
CGCATCCTGCTTTTTGAAGGGAAAATACAGCTGCGGGTGAGGGCGGAACACTTGAGCAGGGACAGGAGTTACCAC

Alignment

ORF - retro_ggor_2505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.13 %
• Parental protein coverage: 75.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLSSVMTIVKSRPFREKQGKILLEGRRLISDALKAGAVPKMFFFSRLEYLKELPVDKLKGVSLIKVKFED
          R..SVMT.VKSRPFREKQGKILL.GRRLI.D.LKAGAV.K.FF.S.L.Y.K.L..DKLKGVSLIK.KFED
Retrocopy RTCSVMTLVKSRPFREKQGKILLKGRRLIADDLKAGAVLKVFFSSHL*YIKKLLIDKLKGVSLIKMKFED

Parental  IKDWSDLVTPQG-IMGIFAKPDHVKMTYPKTQLQHSLPLLLICDNLRDPGNLGTILRSAAGAGCSKVLLT
          IK.WS.LV.PQ..IMGIFAKPDHV.MTYPKTQL.HSLPLLLICD.L.DPGNLGTILRS.AG.GCSKVLLT
Retrocopy IKGWSNLVMPQE<IMGIFAKPDHVNMTYPKTQL*HSLPLLLICDSLCDPGNLGTILRSPAGEGCSKVLLT

Parental  -KGCVDAWEPKVLRAGMGAHFRMPIINNL-EWETVPNYLPPDTRVYVADNCGLYAQAEMSNKASDHGWVC
          .KGCVDAWEPKVL.A.MGAHF..PIINNL.E.ETVPNYL.PDT.V.VADN..LYAQA.MSNKA.D.GWV.
Retrocopy LKGCVDAWEPKVLQAAMGAHFQVPIINNL<ENETVPNYLLPDTQVCVADN*SLYAQAQMSNKARDYGWV*

Parental  DQRVMKFHKYEEEEDVETGASQDWLPHVEVQSYDSDWTEAPAAVVIGGETYGVSLESLQLAESTGGKRLL
          D.R..KFHKYEE....ETGAS...LP..EVQSYD.DWTEAPAAVV.GGETYG..LESL.LAES..GKRLL
Retrocopy DWRFLKFHKYEEKQGLETGASKGLLPVIEVQSYDLDWTEAPAAVVVGGETYGMILESL*LAESPAGKRLL

Parental  IPVVPGVDSLNSAMAASILLFEGKRQLRGRAEDLSRDRSYH
          IPV.PGVDSLNSAMAA.ILLFEGK.QLR.RAE.LSRDRSYH
Retrocopy IPVAPGVDSLNSAMAARILLFEGKIQLRVRAEHLSRDRSYH

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	0.05 RPM	15.25 RPM
SRP007412_cerebellum	0.00 RPM	11.50 RPM
SRP007412_heart	0.00 RPM	12.13 RPM
SRP007412_kidney	0.00 RPM	11.20 RPM
SRP007412_liver	0.00 RPM	9.63 RPM
SRP007412_testis	0.10 RPM	24.14 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_2505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2505 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3704
Pongo abelii	retro_pabe_3149
Macaca mulatta	retro_mmul_1709
Callithrix jacchus	retro_cjac_3130

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021701	1 retrocopy	retro_cjac_3130,
Homo sapiens	ENSG00000171861	1 retrocopy	retro_hsap_3704,
Gorilla gorilla	ENSGGOG00000015518	1 retrocopy	retro_ggor_2505 ,
Macaca mulatta	ENSMMUG00000011423	1 retrocopy	retro_mmul_1709,
Nomascus leucogenys	ENSNLEG00000000570	1 retrocopy	retro_nleu_180,
Pongo abelii	ENSPPYG00000007762	1 retrocopy	retro_pabe_3149,