RetrogeneDB ID: retro_ptro_1967

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:11084319..11085188(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSPTRG00000031310
• Aliases: None
• Description: None

Sequence

>retro_ptro_1967
ATGGATTTATCAGGAGTGAAAAAGAAGAGCTTGCTAGGAGTCAAAGAAAATAATAAAAAATCCAGCACTAGGGCCCCTTC
ACCTACCAAACGCAAAGACCGCTCAGATGAGAAGTCCAAGGATCGCTCAAAAGATATAGGGGCCACCAAGGAGTCGAGTA
AGAAGGATCGCGGCCGGGACAAAACGCGAAAGAGGCGTAGCGCTTCCAGTGGTAGCAGCAGTACCAGGTCTCGGTCCAGC
TCGACTTCCAGCCCAGGCTCCAGCACCAGCACTGGCTCAAGCAGTGGCTCCAGCTCTTCCTCAGCATCCAGCCGCTCAGG
AAGCTCCAGCACCTCCCGCAGCTCCAGCTCTAGCAGCTCTTCTGGCTCTCCAAGTCCTTCTCGGCGCAGACACGACAACA
GGAGGCGCTCCCGCTCCAAATCCAAACCACCTAAAAGAGATGAAAAGGAGAGGAAAAGGCGGAGCCCATCTCCTAAGCCC
ACCAAAGTGCACATTGGGAGACTCACCAGGAATGTGACAAAGGATCACATCATGGAGATATTTTCCACCTATGGGAAAAT
TAAAATGATTGACATGCCCGTGGAAAGGATGCAACCCCATCTGTCCAAAGGCTATGCGTACGTAGAGTTTGAGAATCCAG
ATGAAGCTGAGAAGGCGCTGAAGCACATGGATGGAGGACAAATTGATGGCCAGGAGATCACTGCCACCGCCGTGCTGGCC
CCCTGGCCTAGGCCACCCCCCAGGAGATTCAGCCCTCCCAGGAGAATGTTGCCACCACCGCCTATGTGGCGCAGGTCTCC
CCCACGGATGAGGAGATGGTCCCGCTCACGAGGCGCAGGTCCCCCGTGCGCCGGAGATCACGGTCCCCG

Alignment

ORF - retro_ptro_1967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.13 %
• Parental protein coverage: 95.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDKGTTKESSEKDRGRDKTRKRRSASS
          MDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKD.G.TKESS.KDRGRDKTRKRRSASS
Retrocopy MDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDIGATKESSKKDRGRDKTRKRRSASS

Parental  GSSSTRSRSSSTSSSGSSTSTGSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSK
          GSSSTRSRSSST.............GSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSK
Retrocopy GSSSTRSRSSSTXXXXXXXXXXXXXGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSK

Parental  SKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEF
          SKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERM.PHLSKGYAYVEF
Retrocopy SKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMQPHLSKGYAYVEF

Parental  ENPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRS-PRR
          ENPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRR.SRS..RR
Retrocopy ENPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRWSRS<TRR

Parental  RSPVRRRSRSP
          RSPVRRRSRSP
Retrocopy RSPVRRRSRSP

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	1.27 RPM	73.16 RPM
SRP007412_cerebellum	0.18 RPM	61.09 RPM
SRP007412_heart	0.12 RPM	20.23 RPM
SRP007412_kidney	0.05 RPM	37.42 RPM
SRP007412_liver	0.10 RPM	24.78 RPM
SRP007412_testis	0.32 RPM	40.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1967 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1967 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1967 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2911
Gorilla gorilla	retro_ggor_2016

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004866	4 retrocopies	retro_chof_1587, retro_chof_1985, retro_chof_2272, retro_chof_493,
Cavia porcellus	ENSCPOG00000002066	2 retrocopies	retro_cpor_363, retro_cpor_953,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Pan troglodytes	ENSPTRG00000031310	1 retrocopy	retro_ptro_1967 ,
Pteropus vampyrus	ENSPVAG00000005105	1 retrocopy	retro_pvam_296,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,