RetrogeneDB ID: retro_ptro_1014

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:46984519..46986300(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RLIM
• Ensembl ID: ENSPTRG00000022037
• Aliases: RLIM, RNF12
• Description: None

Sequence

>retro_ptro_1014
ATGGAAAACTCAGTTTCTAACGACAAAGGAAGTGGTGATCAGTCTTCAGCACAGTGCAGAAGTCAGATGGACCGATTGGA
TCGGGAAGAAGCTTTCTATCCATTTGTAAATAACCTGAGTGAAGAAGATTATAGGCTTATGGAGATAATAATTTGCTAGG
CACCCCAGGTGAAAGTACTGAGGAAGAGTTGCTGAGAAGACTACAGCAAACTAAAGAAGGCCCACCACTGCAAAACTCAG
GTGAAAATAGAGAAGGAGACTCTTCAGATGGTGTGTCTAATGGTGACTCTATAATAGACTGGCTTAACTCTGTCAGACAA
ACTGGAAATACAACAAGAAGTGGGCAAAGAGGAAACCAATCTTGGAGAGCAGTGAGCCGGACTAATCCAAACAGCGGTAA
TTTCAGATTCAGTTTAGAGATAAATGTTAACAGTAATAATGGGAGCCAAAATTCAGAGAATGAAAATGAGCCATCTGCAA
GACGTTCTAGTGGAGAAAATGTGGAAAACAACAGCCAAAGGCAAGTGGAAAACCCACGATCTGAATCAACATCTGCAAGG
CCATCTAGATCAGAACGAAATTCAACTGAAGCATTAACAGAAGTCCCACCTACCAGAGGTCGGGGAGGGCAAGAAGCAGG
AGCCCAGACCGTGGGAGAACCAGAGCAAGAGCTGAGAGAAGTAGGTCACCTCTGCATCCAATGAGTGAAATTCCACGAAG
ATCTCATCATAGTATCTCATCTCAGACTTTTGAACATCCTTTGGTAAATGAGATGGAGGGAAGTTCTAGAACCCGGCCCT
GTGTGACATTGAGACAGCAAATATCTGGGCCTGAGTTGCTAAGTAGAGGTCTTTTTGCAGCTTCTGGAAAAAGAAATGCC
TCTCAAGCAGCAGGTTCTTCAGACACAGCTGCCAATGGTGAATCTACAGGATCAGCACAGAGACCTCTAACCATAGTCCT
TGATCTTCAAGTAAAAAGAGTTAGTCCTGGAGAATATTGGCAGAGAGATAGCATAGCCAGCAGAACTCGGTCTAGGTCTC
AGAGGCCAAACAACACTATCACCTATGAAAGTGAGCGAGGAGGTTTCAGGCATATGTTTTCACGTTCTGAGTGGGCAGGT
GTGAGAACCTATGTCAGTAGCACCAGAATCCCCATTTGTAGAATCTTAAATACTGGTTTATGTGAGACTACATCTGTTGC
AATTCAGACGATGTTAAGGCAGATAATGACAGGTTTTGGTGAGATAAGCTATTTTATGTACAGTGATAGCGACTCAGAGC
CTACTGGCTCAGTCCCAAATCAAAATATGGAAAGGGCAGAGTCACGGAGTGGAAGAGGGGGTTCTGGTGGTGGTAGTAGT
TCTGGTTCCAGTTCGAGTTCCAGTTCAAGTTCCAGTTCCAGTTCCAGTCCTAGTTCCAGTTCCGGTGGTGAAAGCTCAGA
AACTAGCTCAGATTTATTTGAAGGCAGTAATGAAGGAAGCTCATCATCAGGCTCATCAGGTGCCAGGCGAGAGGGTCGAC
ATACGGCCCCAGTCATATTTCATTAAAGTGGCTCTTTGCCCTTCCTAGCCTGGCTCAGTTTTCCTCTTAAATGAGGATGA
TGATGACCAACCTAGAGGACTCACTAAAGAACAGATTGACAACTTGGCAATGAGAAGTTTTGGTGAAAATGGTGCATTAA
AAACCTGTAGTGTTTGCATTACAGAATATACAGAAAGCAACAAACTTCGTAAACTACCTTGTTCCCATGAGTACCATGTC
CACTGACTGCATCGATCGCTG

Alignment

ORF - retro_ptro_1014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 96.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMR-DNNLLGTPGESTEEELLRRLQ
          MENS.SNDKGSGDQS.AQ.RSQMDRLDREEAFY.FVNNLSEEDYRLM..DNNLLGTPGESTEEELLRRLQ
Retrocopy MENSVSNDKGSGDQSSAQCRSQMDRLDREEAFYPFVNNLSEEDYRLME<DNNLLGTPGESTEEELLRRLQ

Parental  QIKEGPPPQNSDENRGGDSSDDVSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSGDFRFSL
          Q.KEGPP.QNS.ENR.GDSSD.VSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSG.FRFSL
Retrocopy QTKEGPPLQNSGENREGDSSDGVSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSGNFRFSL

Parental  EINVNRNNGSQNSENESEPSARRSSGENVENNSQRQVENPRSESTSARPSRSERNSTEALTEVPPTRGQR
          EINVN.NNGSQNSENE.EPSARRSSGENVENNSQRQVENPRSESTSARPSRSERNSTEALTEVPPTRG..
Retrocopy EINVNSNNGSQNSENENEPSARRSSGENVENNSQRQVENPRSESTSARPSRSERNSTEALTEVPPTRGRG

Parental  -RARSRSPDHRRTRARAERSRSPLHPMSEIPRRSHHSISSQTFEHPLVNETEGSSRTRHHVTLRQQISGP
          .RARSRSPD..RTRARAERSRSPLHPMSEIPRRSHHSISSQTFEHPLVNE.EGSSRTR..VTLRQQISGP
Retrocopy <RARSRSPDRGRTRARAERSRSPLHPMSEIPRRSHHSISSQTFEHPLVNEMEGSSRTRPCVTLRQQISGP

Parental  ELLSRGLFAASGTRSASQGAGSSDTAASGESTGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQ
          ELLSRGLFAASG.R.ASQ.AGSSDTAA.GESTGS.QRP.TIVLDLQV.RV.PGEY.QRDSIASRTRSRSQ
Retrocopy ELLSRGLFAASGKRNASQAAGSSDTAANGESTGSAQRPLTIVLDLQVKRVSPGEYWQRDSIASRTRSRSQ

Parental  TPNNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSY
          .PNNT.TYESERGGFR..FSRSE.AGVRTYVS..RIPI.RILNTGL.ETTSVAIQTMLRQIMTGFGE.SY
Retrocopy RPNNTITYESERGGFRHMFSRSEWAGVRTYVSSTRIPICRILNTGLCETTSVAIQTMLRQIMTGFGEISY

Parental  FMYSDSDSEPTGSVSNRNMERAESRSGRGGSGGGSSSGSSSSSSSSSSSSSSSSPSSSSGGESSETSSDL
          FMYSDSDSEPTGSV.N.NMERAESRSGRG..G.G..S.S....................GGESSETSSDL
Retrocopy FMYSDSDSEPTGSVPNQNMERAESRSGRG--GSGGGSSSXXXXXXXXXXXXXXXXXXXXGGESSETSSDL

Parental  FEGSNEGSSSSGSSGARREGRHRAPVTFDESGSLPFL-SLAQF-FLLNEDDDDQPRGLTKEQIDNLAMRS
          FEGSNEGSSSSGSSGARREGRH.APV.F..SGSLPFL.SLAQF.FLLNEDDDDQPRGLTKEQIDNLAMRS
Retrocopy FEGSNEGSSSSGSSGARREGRHTAPVIFH*SGSLPFL<SLAQF<FLLNEDDDDQPRGLTKEQIDNLAMRS

Parental  FGENDALKTCSVCITEYTEGNKLRKLPCSHEYHVHCIDRWL
          FGEN.ALKTCSVCITEYTE.NKLRKLPCSHEYHVH...R.L
Retrocopy FGENGALKTCSVCITEYTESNKLRKLPCSHEYHVH*LHRSL

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	0.02 RPM	10.64 RPM
SRP007412_cerebellum	0.11 RPM	24.95 RPM
SRP007412_heart	0.00 RPM	14.25 RPM
SRP007412_kidney	0.10 RPM	14.25 RPM
SRP007412_liver	0.07 RPM	7.27 RPM
SRP007412_testis	3.79 RPM	14.33 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1014 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1014 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1014 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1495
Pongo abelii	retro_pabe_1245
Macaca mulatta	retro_mmul_2139

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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	ENSG00000131263	1 retrocopy	retro_hsap_1495,
Macaca mulatta	ENSMMUG00000009249	1 retrocopy	retro_mmul_2139,
Pongo abelii	ENSPPYG00000020481	1 retrocopy	retro_pabe_1245,
Pan troglodytes	ENSPTRG00000022037	1 retrocopy	retro_ptro_1014 ,