RetrogeneDB ID: retro_pabe_1245

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:46340882..46342411(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RLIM
• Ensembl ID: ENSPPYG00000020481
• Aliases: None
• Description: ring finger protein, LIM domain interacting [Source:HGNC Symbol;Acc:13429]

Sequence

>retro_pabe_1245
ATGGAAAACTCAGATTCTAACGACAAAGGAAGTGGTGATCAGTCTGCAGCACAGCGCAGAAGTCAGATGGACCGATTGGA
TCGGGAAGAAGCTTTCTATCCATTTGTAAATAACCTGAGTGAAGAAGATTATAGGCTTATGAGAGATAATAATTTGCTAG
GCACCCCAGGTGAAAGTACTGAGGAAGAGTTGCTGAGAAGACTACAGCAAATTAAAGAAGGCCCACCACCGCAAAACTCA
GGTGAAAATAGAGGAGGAGACTCTTCAGATGATGTGTCTAATGGTGACTCTATAATAGACTGGCTTAACTCTGTCAGACA
AACTGGAAATACAACAAGTGGGCAAAGAGGTAACCAATCTTGGAGAGCAGTGAGCCGGACTAATCCAAACAGTGGTGATT
TCGGATTCAGTTTAGAGATAAATGTTAACAGTAATAATGGGAGCCAAAATTCAGAGAATGAAAATGAGCCATCTGCAAGA
CGTTCTAGTGGAGAAAATGTGGAAAACAACAGCCAAAGGCAAGTGGAAAACCCATGATCTGAATCAACATCTTCAAGGCC
ATCTAGATCAGAACGAAATTCAACTGAAGCATTAACAGAAGTCCCACCTACCAGAGGTCAGAGGAGGGCAAGAAGCAGGA
GCCCAGACCGTGGGAGAACCAGAGCAAGAGCTGAGAGAAGTAGTTCACCTCTGCATCCAATGAGTGAAATTCCACGAAGA
TCTCATCATAGTATCTCATCTCAGACTTTTGAACATCCTTTGGTAAATGAGATGGAGGGAAGTTCTAGAACCCGGCCCTG
TGTGACATTGAGACAGCAAATATCTGGGCCTGAGTTGCTAAGTAGAGGTCTTTTTGCAGCTTCTGGAACAAGAAATGCCT
CTCAAGGAGCAGGTTCTTCAGACACAGCTGCCAATGGTAAATCTACAGGATCAGCACAGAGACCTCCAACCATAGTCCTT
GATCTTCAAGTAAAAAGAGTTCGTCCTGCAGAATATCGGCAGAGAGATAGCACAGCCAGCAGAACTCGGTCTAGGTCTCA
GAGGCCAAACAACACTGTCACCTATGAAAGTGAACGAGGAGGTTTTAGGCGTACGTTTTCACGTTCTGAGTGGGCAGGTG
TGAGAACGTATGTCAGTACCATCAGAATTCCCATTCGTAGAATCTTAAATACTGGTTTATGTGAGACTACATCTGTTGCA
ACTCAGACCATGTTAAGGCGGATAATGACAGGTTTTGGTGAGTTAAGCTATTTTATGTACAGTGATAGCAACTCAGAGCC
TACTGGCTCAGTCCCAAATCAAAATATGGAAAGGGCAGAGTCACGGAGTGGAAGGGGGGTTCTGGTGGTGGTAGTAGTTC
TGGTTCCAGTTCCAGTTCCAGTCCTAGTTCCAGTTCCGGTGGTGAAAGTTCAGAAACTAGCTCAGATTTATTTGAAGGCA
GTAATGAAGGAAGCTCATCATCAGGCTCATCAGGTGTCAGGCGAGAGGGTCGACATAGGGCCCCAGTCATATTTGATGAA
AGTGGCTCT

Alignment

ORF - retro_pabe_1245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.74 %
• Parental protein coverage: 81.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQ
          MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFY.FVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQ
Retrocopy MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFYPFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQ

Parental  IKEGPPPQNSDENRGGDSSDDVSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSGDFRFSLE
          IKEGPPPQNS.ENRGGDSSDDVSNGDSIIDWLNSVRQTGNTT.SGQRGNQSWRAVSRTNPNSGDF.FSLE
Retrocopy IKEGPPPQNSGENRGGDSSDDVSNGDSIIDWLNSVRQTGNTT-SGQRGNQSWRAVSRTNPNSGDFGFSLE

Parental  INVNRNNGSQNSENENEPSARRSSGENVENNSQRQVENPRSESTSARPSRSERNSTEALTEVPPTRGQRR
          INVN.NNGSQNSENENEPSARRSSGENVENNSQRQVENP.SESTS.RPSRSERNSTEALTEVPPTRGQRR
Retrocopy INVNSNNGSQNSENENEPSARRSSGENVENNSQRQVENP*SESTSSRPSRSERNSTEALTEVPPTRGQRR

Parental  ARSRSPDHRRTRARAERSRSPLHPMSEIPRRSHHSISSQTFEHPLVNETEGSSRTRHHVTLRQQISGPEL
          ARSRSPD..RTRARAERS.SPLHPMSEIPRRSHHSISSQTFEHPLVNE.EGSSRTR..VTLRQQISGPEL
Retrocopy ARSRSPDRGRTRARAERSSSPLHPMSEIPRRSHHSISSQTFEHPLVNEMEGSSRTRPCVTLRQQISGPEL

Parental  LSRGLFAASGTRNASQGTGSSDTAANGESTGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQTP
          LSRGLFAASGTRNASQG.GSSDTAANG.STGS.QRPPTIVLDLQV.RVRP.EYRQRDS.ASRTRSRSQ.P
Retrocopy LSRGLFAASGTRNASQGAGSSDTAANGKSTGSAQRPPTIVLDLQVKRVRPAEYRQRDSTASRTRSRSQRP

Parental  NNTVTYESERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFM
          NNTVTYESERGGFRRTFSRSE.AGVRTYVSTIRIPIRRILNTGL.ETTSVA.QTMLR.IMTGFGELSYFM
Retrocopy NNTVTYESERGGFRRTFSRSEWAGVRTYVSTIRIPIRRILNTGLCETTSVATQTMLRRIMTGFGELSYFM

Parental  YSDSDSEPTGSVSNRNMERAESRSGR-GGSGGGSSSGSSSSSSSSSSSSSSSSSSSS---PSSSSGGESS
          YSDS.SEPTGSV.N.NMERAESRSGR.GGSGGGS.................SS..SS.....S..G..SS
Retrocopy YSDSNSEPTGSVPNQNMERAESRSGR<GGSGGGSXXXXXXXXXXXXXXXGESSETSSDLFEGSNEGSSSS

Parental  ETSSDLFEGSNEGSSSSGSSGA
          ..S....EG..........SG.
Retrocopy GSSGVRREGRHRAPVIFDESGS

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	10.78 RPM
SRP007412_cerebellum	0.00 RPM	10.09 RPM
SRP007412_heart	0.00 RPM	4.61 RPM
SRP007412_kidney	0.00 RPM	5.80 RPM
SRP007412_liver	0.00 RPM	4.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1245 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1245 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1495
Pan troglodytes	retro_ptro_1014
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,