RetrogeneDB ID: retro_ptro_2720

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:123596653..123597360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRS2
• Ensembl ID: ENSPTRG00000017774
• Aliases: MRS2, MRS2L
• Description: None

Sequence

>retro_ptro_2720
TCTGACCTGTGTGGGCCCGCCGGCTCTGCGTAGCAGGTGCAATGCACGGGTTTAGAACTTCTGATGTCTCTCAAGCCACT
GTAGGCAGTGTAGCCCCAGTATTTACCGCAACAAAATTTGACAAACAGGGAAATGTTACTCCTTTTGAAAGGAAGAAAAC
TGACTTATATCAAGAGTTAGGTCTTCAAGCCAGAGACTTGAGATTTCAGCATGTAGTGAGCATCACAACCAGAAACGGCA
GGTTTATCATGACAATGGAGTATTTGAAAGCTGTGATAACTCCAGAGTGTCTCCTGATATTAGATGATGGTAATTTAAAC
TTAGAGCAATGGCTGTTCTGGGAACTCCCTTCACAGTTGTCTGGAGAGGGTCAACCTGTTACATACTCTTTACCTTTTGA
GTTTAGTGCTATGGAAGCACCCCTGAAATACTGGATCAACCCCCTTTAGAGGAAACGTAGCGTTTTGCAGACACTGACTT
TTGAGACCTTAGAAGCTTTCAAACATTCTTCTGTGGACAAAAGCTAACCACATATTTCACTACAGAATGACAAAAGTCTA
TCAGAGTTAGAAACAGATATTAAAATTTTCCAAGAGTCAATTTTGGAGATCTTGGGTGAGGAAAAGTTACTAGAAGAGCT
CTGTCTATCAAAATGGAGTGACCCACCAGTCTTTGAAAAGAGCAGTACTGGGATTCGCCATGCAGAA

Alignment

ORF - retro_ptro_2720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.92 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQLCGPD-RLRVAGEVRRFRTSDVSQATLASVAPVFTVTKFDKQGNVTSFERKKTELYQELGLQARDLRF
          ..LCGP..RL.VAG....FRTSDVSQAT..SVAPVFT.TKFDKQGNVT.FERKKT.LYQELGLQARDLRF
Retrocopy SDLCGPA<RLCVAGAMHGFRTSDVSQATVGSVAPVFTATKFDKQGNVTPFERKKTDLYQELGLQARDLRF

Parental  QHVMSITVRNNRIIMRMEYLKAVITPECLLILDYRNLNLEQWLFRELPSQLSGEGQLVTYPLPFEFRAIE
          QHV.SIT.RN.R.IM.MEYLKAVITPECLLILD..NLNLEQWLF.ELPSQLSGEGQ.VTY.LPFEF.A.E
Retrocopy QHVVSITTRNGRFIMTMEYLKAVITPECLLILDDGNLNLEQWLFWELPSQLSGEGQPVTYSLPFEFSAME

Parental  ALLQYWINTLQGKLSILQPLILETLDALVDPKHSSVDRSKLHILLQNGKSLSELETDIKIFKESILEILD
          A.L.YWIN.L..K.S.LQ.L..ETL.A....KHSSVD.S..HI.LQN.KSLSELETDIKIF.ESILEIL.
Retrocopy APLKYWINPL*RKRSVLQTLTFETLEAF---KHSSVDKS*PHISLQNDKSLSELETDIKIFQESILEILG

Parental  EEELLEELCVSKWSDPQVFEKSSAGIDHAE
          EE.LLEELC.SKWSDP.VFEKSS.GI.HAE
Retrocopy EEKLLEELCLSKWSDPPVFEKSSTGIRHAE

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	15.03 RPM
SRP007412_cerebellum	0.00 RPM	22.37 RPM
SRP007412_heart	0.03 RPM	33.34 RPM
SRP007412_kidney	0.08 RPM	28.06 RPM
SRP007412_liver	0.00 RPM	13.45 RPM
SRP007412_testis	0.63 RPM	7.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2720 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2720 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4006
Gorilla gorilla	retro_ggor_2689
Macaca mulatta	retro_mmul_2312

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006424	1 retrocopy	retro_dnov_1486,
Equus caballus	ENSECAG00000013105	1 retrocopy	retro_ecab_1032,
Homo sapiens	ENSG00000124532	1 retrocopy	retro_hsap_4006,
Gorilla gorilla	ENSGGOG00000009098	1 retrocopy	retro_ggor_2689,
Macaca mulatta	ENSMMUG00000001018	2 retrocopies	retro_mmul_2312, retro_mmul_878,
Pongo abelii	ENSPPYG00000016278	1 retrocopy	retro_pabe_939,
Pan troglodytes	ENSPTRG00000017774	1 retrocopy	retro_ptro_2720 ,