RetrogeneDB ID: retro_ptro_691

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:47001175..47002414(+)
• Located in intron of: ENSPTRG00000004839

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXR1
• Ensembl ID: ENSPTRG00000015656
• Aliases: None
• Description: None

Sequence

>retro_ptro_691
ACCGTCTTTAAATGCACAGTGGATTTTCCTGAGGATATGAGAGAGGCGTGTGCTAATGAAAATGCACACAAAGATTTTAA
GAAAGCAGTAGGAGCATGCAGAATTTTTTACCATCCAGAAACAACACAGCTAATGACACTGTCTGCCAGTGAAGCAACTG
TGAAGAAAGTAAACATCTTGAGTGACATGCGTTTGTGAAGTATTTGTATGAAGTTGATGCTTATGACCAGAAATGAAGAG
ATCACCAAGCATTCAGAATGCACAAAACAACTTGCAGCAGCTTTTCCTGAGGAATTTGTTGTGAGAGAAAATTTAATGAG
TGTGGCAATAGGAACACATGGTAGTAACATTCAGCAAGCTAGGAAGGTTCCTGGAGTTACCGCATTGAGCTAGATGAAGA
CACTGGAACATTTAGAATCTATAGAGAGTGCTGGTGCTGTAAAAAAGGCTAGAGGTTTCTTGGAATTTGTGGAGGATTTT
ATTCAGGTTTCTAAGAATCTCATTGGAAAAGTAATTGGAAAAAATGGCAAAGTTATTCAAGAAATAGTGGACAAATCTGA
TATGGTTCGGGTGAGAATTGAAGGGGACAGTGAAAATAAAACTACTCAGAGAAGACAGTATGATTCCATTTGTATTTGTT
GGCACTAAAGAAACCATTGGAAATGTGCAAGTTCTTTTAAAGTACCATATTGCTTATCTAAAGGAAGTAGAACAGCTAAG
AATGGAATGCCTACAGATTAATGAGCAGCCATAACAGATTGGTTCTAGGTCTCATAGTGGAAGAGGCAGAGGTTGTCAGG
GCCCTAATTACACCTCCAGTTATGGTACAAATTCTGAGCTGTCTAACCCCTCTGAAATAGAATCTGAGGGTAAAGACAAG
CTGAGTGATTTGGTCACTGAAGAAGATGATCGAGACAGCCGACATCAGCGTGACAGCAGGAGATGCCCAGGAGGAAGATG
CAGAAGTGTTTCAGGGGGTCGAGGTCGTGGTGGACCACGTGGTGGCAAATCCTCCATCAGTTCTGTGCCCAAAGATCCAG
ACAGCAATCCATACAGCGTACTTGATAATCAGAATCAGATCAGACTGCAGACACTGATGCCAGCAAATCTCATCACAGTA
CTAATCGTCATACGAGGTCTCGTAGACGAAGGACTGATGAAGATGTTGTTCTGATGGATGGAATGACTGAATCTGATACA
GCTTCAGTTACTGAAAATGGGCTAGGCAAAATATGTGAT

Alignment

ORF - retro_ptro_691 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.29 %
• Parental protein coverage: 66.83 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRT
          T.FKCTVD.PED.REACANENAHKDFKKAVGACRIFYHPETTQLM.LSASEATVK.VNILSDM.L.SI..
Retrocopy TVFKCTVDFPEDMREACANENAHKDFKKAVGACRIFYHPETTQLMTLSASEATVKKVNILSDMRL*SICM

Parental  KLMLMSRNEEATKHLECTKQLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTA-IELDEDTGTFR
          KLMLM.RNEE.TKH.ECTKQLAAAF.EEFVVRE.LM..AIGTHGSNIQQARKVPGVTA.IELDEDTGTFR
Retrocopy KLMLMTRNEEITKHSECTKQLAAAFPEEFVVRENLMSVAIGTHGSNIQQARKVPGVTA<IELDEDTGTFR

Parental  IYGESADAVKKARGFL-EFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNEN-KLPREDG
          IY.E.....KK...FL.EFVEDFIQV..NL.GKVIGKNGKVIQEIVDKS..VRVRIEGD.EN.KL.RED.
Retrocopy IYRE-CWCCKKG*RFL>EFVEDFIQVSKNLIGKVIGKNGKVIQEIVDKSDMVRVRIEGDSEN>KLLREDS

Parental  MVPFVFVGTKESIGNVQVLLEYHIAYLKEVEQLRMERLQIDEQLRQIGSRSYSGRGRGRRGPNYTSGYGT
          M.PFVFVGTKE.IGNVQVLL.YHIAYLKEVEQLRME.LQI.EQ..QIGSRS.SGRGRG..GPNYTS.YGT
Retrocopy MIPFVFVGTKETIGNVQVLLKYHIAYLKEVEQLRMECLQINEQP*QIGSRSHSGRGRGCQGPNYTSSYGT

Parental  NSELSNPSETESERKDELSDWSLAGEDDRDSRHQRDSRRRPGGRGRSVSGGRGRGGPRGGKSSISSVLKD
          NSELSNPSE.ESE.KD.LSD.....EDDRDSRHQRDSRR.PGGR.RSVSGGRGRGGPRGGKSSISSV.KD
Retrocopy NSELSNPSEIESEGKDKLSD-LVTEEDDRDSRHQRDSRRCPGGRCRSVSGGRGRGGPRGGKSSISSVPKD

Parental  PDSNPYSLLDN-TESDQTADTDASESHHSTNRRRRSRRRRTDEDAVLMDGMTESDTASVNENGLVTVAD
          PDSNPYS.LDN..ESDQTADTDAS.SHHSTNR..RSRRRRTDED.VLMDGMTESDTASV.ENGL....D
Retrocopy PDSNPYSVLDN<SESDQTADTDASKSHHSTNRHTRSRRRRTDEDVVLMDGMTESDTASVTENGLGKICD

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	0.16 RPM	57.59 RPM
SRP007412_cerebellum	0.39 RPM	71.45 RPM
SRP007412_heart	0.12 RPM	171.61 RPM
SRP007412_kidney	0.29 RPM	92.55 RPM
SRP007412_liver	0.29 RPM	63.70 RPM
SRP007412_testis	3.27 RPM	823.15 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_691 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_691 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_691 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000012105	1 retrocopy	retro_mmul_859,
Nomascus leucogenys	ENSNLEG00000005928	1 retrocopy	retro_nleu_197,
Ochotona princeps	ENSOPRG00000009223	2 retrocopies	retro_opri_61, retro_opri_779,
Pan troglodytes	ENSPTRG00000015656	1 retrocopy	retro_ptro_691 ,