RetrogeneDB ID: retro_ptro_474

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:21968217..21969152(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPR
• Ensembl ID: ENSPTRG00000000324
• Aliases: HNRNPR, HNRPR
• Description: None

Sequence

>retro_ptro_474
GCTGGAAAAGTAAAAGTATGGGGAAATGTAGTTACAGTCGAATGGGCTGACCCTGTGAAGAACCATATCCAGAAGTCATG
GCTAAGGTAAAAGTATTCTTTGTGAGAAACTTGGGCACAGACAAAATATTGGAAAAGTCATTTTCTGAATTTGGAGTACT
CCAAAGAGTAAATAAGTTGAAAGATTATGCATTTGTTCATTCTGAAGACAGACGAGCAGCTGTTATGGCTATGGATGAAA
TGAATGGCAAAGAAACAGAAGGGGAAGAACTTGAAATAGTCTTAGCCAAGCCACCAAACAAGAAAAGGAAAGAGCGCCAA
GCTGCTAGACAGGCCTCCAGAAGCACTGCATATGAAGATTATCACTACACCCTCCTCCTCGCATGCCGCTTCCGATTAGA
GGTTGGGGGAGAGGTGGATATGGCTAACCTCCAGATTACTATGGCATGAAGATTACTACGGTTATGATTACCACATCTAT
CATGGAGGTTACGAAGTCTCCCTACTATGGCTATGATGATGGCTATGCGGTAAGAGGAAGAGGAGGAAGGGGAGGGCAGA
GTGCTCCACCACCACCAAGGGGGAGGGGAGCACCACCTCCAAGAGGTAGAGCTGGCTATTCACAAAAGGGGGCACCTTTG
GGACCACCACGAGGCTGTAGGGGTGGCAGAGGGGGTCCTGCACAACAGCAGAGAGGCCGTGGCCGTGGTTCCCGTGGATC
TCAGGGCAATCAGGGGACAACGTAGGAGGCAAGAGAAGGCAGATGCTTACAACCAACCTGATTCCAAGCATCGTCAGACC
AACAAACAACAGAACTGGGTCTCTCAACCCATCGCTCAGCAGCCGCTTCAGCAAGGTGGTGACTATTCTGGTAACTATGG
TTACAATAATGACAACCAGGAATTTTATCAGGATACTTATGGGCAACAGTGGAAG

Alignment

ORF - retro_ptro_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.69 %
• Parental protein coverage: 51.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SGKVKVWGNVVTVEWADPV-EEPDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFV
          .GKVKVWGNVVTVEWADPV.EEP.PEVMAKVKV.FVRNL....T..ILEKSFSEFG.L.RV.KLKDYAFV
Retrocopy AGKVKVWGNVVTVEWADPV<EEPYPEVMAKVKVFFVRNLG---TDKILEKSFSEFGVLQRVNKLKDYAFV

Parental  HFEDRGAAVKAMDEMNGKEIEGEEIEIVLAKPPDKKRKERQAARQASRSTAYEDYYY-HPPPRMPPPIRG
          H.EDR.AAV.AMDEMNGKE.EGEE.EIVLAKPP.KKRKERQAARQASRSTAYEDY.Y.HPPPRMP.PIRG
Retrocopy HSEDRRAAVMAMDEMNGKETEGEELEIVLAKPPNKKRKERQAARQASRSTAYEDYHY<HPPPRMPLPIRG

Parental  RGRGGGRGGYGYPPDYYG-YEDYYDDYYGYDYHDYRGGYE-DPYYGYDDGYAVRGRGGGRGGRGAPPPPR
          .GRGG....YG.PPDYYG..EDYY....GYDYH.Y.GGYE..PYYGYDDGYAVRGR.GGRGG..APPPPR
Retrocopy WGRGG----YG*PPDYYG<HEDYY----GYDYHIYHGGYE>SPYYGYDDGYAVRGR-GGRGGQSAPPPPR

Parental  GRGAPPPRGRAGYSQRGAPLGPPRGSRGGRGGPAQQQ--RGRGSRGSRGNR-GGNVGGKR-KADGYNQPD
          GRGAPPPRGRAGYSQ.GAPLGPPRG.RGGRGGPAQQQ..RGRGSRGS.GN..G.NVGGKR.KAD.YNQPD
Retrocopy GRGAPPPRGRAGYSQKGAPLGPPRGCRGGRGGPAQQQRGRGRGSRGSQGNQ<GDNVGGKR<KADAYNQPD

Parental  SKRRQTNNQQNWGSQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTYGQQWK
          SK.RQTN.QQNW.SQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTYGQQWK
Retrocopy SKHRQTNKQQNWVSQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTYGQQWK

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	53.68 RPM
SRP007412_cerebellum	0.07 RPM	97.58 RPM
SRP007412_heart	0.00 RPM	51.76 RPM
SRP007412_kidney	0.00 RPM	59.10 RPM
SRP007412_liver	0.07 RPM	43.14 RPM
SRP007412_testis	0.11 RPM	68.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_474 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_474 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_651
Gorilla gorilla	retro_ggor_568
Macaca mulatta	retro_mmul_2433

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000125944	1 retrocopy	retro_hsap_651,
Gorilla gorilla	ENSGGOG00000013250	1 retrocopy	retro_ggor_568,
Macaca mulatta	ENSMMUG00000010970	1 retrocopy	retro_mmul_2433,
Monodelphis domestica	ENSMODG00000016144	1 retrocopy	retro_mdom_240,
Mus musculus	ENSMUSG00000066037	1 retrocopy	retro_mmus_458,
Otolemur garnettii	ENSOGAG00000009179	1 retrocopy	retro_ogar_3144,
Procavia capensis	ENSPCAG00000010462	1 retrocopy	retro_pcap_88,
Pan troglodytes	ENSPTRG00000000324	1 retrocopy	retro_ptro_474 ,
Pan troglodytes	ENSPTRG00000018393	1 retrocopy	retro_ptro_1387,
Tupaia belangeri	ENSTBEG00000002251	1 retrocopy	retro_tbel_4256,