RetrogeneDB ID: retro_ptro_425

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:49733302..49734053(+)
• Located in intron of: ENSPTRG00000002509

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSU1
• Ensembl ID: ENSPTRG00000002325
• Aliases: None
• Description: None

Sequence

>retro_ptro_425
ATCTACAACATGCTGTATGTCAATGGCACATTTTCCTTATCCCATACCATACAACTGGTCCTCAGCCATAACAAGCTCAC
AGTGGTGCCACCAAACACAGAAGAACTGAAGAATTTGGAAGTGCTCAACTTCCTTAATAGCCAGATTGAGGAGCTGCCCA
CACAGATCGGCAGCCTTCAGAAACTCAAACACGTGAACCTGGGCATGAATGGGCTAAATACTTTGCCTGAAGGATTTTGC
TTTCTACCCAGCTCTTGACCTTCTGGACTTGATGTACAATTTGAATGAAAATTCTCTTCCTGGAAACTTCATCTACCTTA
CCACCTTCCGTGCACTCTTATGTAAGTGACAATGATTTTGAAATCCTGAAACCAGATATTAGGAAGCTCACAAAGTTGCA
GATACCCAGCTTTAGGGATAACAACCTGATCTTGCAGCCTAGGGAAACTGGGGAGTCTACCCAGCTTAAGGAACTCAACA
TTCAGGGCAACTGCCTGACCCTTCTGCTCCCAGAACTAGGAAACTTATATTTAACTGGTCAGAAGAAGGTATGCAAAGTG
GAGAACAGCCCCTGGGTTACCCCAATTGCTGGCTAGTTCCAGCTTGATGTGTCCTGTGTGTTTGAATGTGTCTGTTCTGA
GACATATGAGTACCTCTATAGCAGCACATGCAGGCAAATCCAGAACCACCAAAAAATAATAATCACAAATCAGAAAAGAT
GAGCTGGAAACACCTGACAGACAGTAACAAA

Alignment

ORF - retro_ptro_425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.62 %
• Parental protein coverage: 90.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ISNMLDVNGLFTLSHITQLVLSHNKLTTVPPNIAELKNLEVLNFFNNQIEELPTQISSLQKLKHLNLGMN
          I.NML.VNG.F.LSH..QLVLSHNKLT.VPPN..ELKNLEVLNF.N.QIEELPTQI.SLQKLKH.NLGMN
Retrocopy IYNMLYVNGTFSLSHTIQLVLSHNKLTVVPPNTEELKNLEVLNFLNSQIEELPTQIGSLQKLKHVNLGMN

Parental  RLNTLPRGFGSLP-ALEVLDLTYNNLSENSLPGNFFYLTTLRAL-YLSDNDFEILPPDIGKLTKLQILSL
          .LNTLP.GF..LP.AL..LDL.YN.L.ENSLPGNF.YLTT.RAL.Y.SDNDFEIL.PDI.KLTKLQI.S.
Retrocopy GLNTLPEGFCFLP>ALDLLDLMYN-LNENSLPGNFIYLTTFRAL>YVSDNDFEILKPDIRKLTKLQIPSF

Parental  RDNDLISLPKEIGELTQLKELHIQGNRLTVLPPELGNLDLTGQKQVFKAENNPWVTPIADQFQLGVSHVF
          RDN.LI..P.E.GE.TQLKEL.IQGN.LT.L.PELGNL.LTGQK.V.K.EN.PWVTPIA..FQL.VS.VF
Retrocopy RDNNLILQPRETGESTQLKELNIQGNCLTLLLPELGNLYLTGQKKVCKVENSPWVTPIAG*FQLDVSCVF

Parental  EYIRSETYKYLYG-RHMQANPEPPKKNNDKSKKISRKPLAAKNR
          E...SETY.YLY...HMQANPEPPK.NN.KS.K.S.K.L...N.
Retrocopy ECVCSETYEYLYS<QHMQANPEPPKNNNHKSEKMSWKHLTDSNK

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	9.15 RPM
SRP007412_cerebellum	0.04 RPM	17.85 RPM
SRP007412_heart	0.00 RPM	25.07 RPM
SRP007412_kidney	0.00 RPM	20.90 RPM
SRP007412_liver	0.00 RPM	35.25 RPM
SRP007412_testis	0.00 RPM	7.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_425 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_425 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_575
Gorilla gorilla	retro_ggor_512
Pongo abelii	retro_pabe_611

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000148484	1 retrocopy	retro_hsap_575,
Gorilla gorilla	ENSGGOG00000028048	1 retrocopy	retro_ggor_512,
Macropus eugenii	ENSMEUG00000006702	1 retrocopy	retro_meug_2092,
Macaca mulatta	ENSMMUG00000016067	1 retrocopy	retro_mmul_712,
Monodelphis domestica	ENSMODG00000009942	1 retrocopy	retro_mdom_338,
Nomascus leucogenys	ENSNLEG00000012444	1 retrocopy	retro_nleu_462,
Pongo abelii	ENSPPYG00000002120	1 retrocopy	retro_pabe_611,
Pan troglodytes	ENSPTRG00000002325	1 retrocopy	retro_ptro_425 ,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649, retro_ptro_1650,
Tarsius syrichta	ENSTSYG00000002386	1 retrocopy	retro_tsyr_730,