RetrogeneDB ID: retro_ptro_1541

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:45693420..45693861(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRTCAP2
• Ensembl ID: ENSPTRG00000001410
• Aliases: None
• Description: keratinocyte associated protein 2 [Source:HGNC Symbol;Acc:28942]

Sequence

>retro_ptro_1541
TTGGTCAGAGGCGCCAATTTGACTCACAGGCAGGGCATGATGGTGGTGGGTACAGACACCTCACTGGCGATCTCCTCCCT
CCTGTCCCTGCTGCTCTTCACTGGGATGCAGATGTAGATCCATCAGCTGGCCTCCACCTAGTGGCTTACCATCCACGGTG
GCCTGCATGGCTCAGGTCTCTTCGTGCTCTCCCTCACTGCCTTCAAGATTCTGGAGAATCTTGTGTTTGGCAAAGGATCC
CAAGCAAATACCTTCCCTGAGATTCTCCTGTGCCTCCTGTTGGCTCTCTTTGCATCTGGCCTCATCCACCGAGTCTGTGT
CACCACCTGCTTCATCTTCTCCGTGATTGGTCTGTGCTACATCAACAAGATCTCCACTCTGTATCAGGCAGCAGCTGCAG
TCCTCACAGGACCTTGGCTCTTGCCAAGGTCACAGGCAAGA

Alignment

ORF - retro_ptro_1541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.7 %
• Parental protein coverage: 91.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LARGAGWTHGRGMMVVGTGTSLALSSLLSLLLFAGMQMYSRQLASTEWLTIQGGLLGSGLFVFSLTAFNN
          L.RGA..TH..GMMVVGT.TSLA.SSLLSLLLF.GMQM...QLAST.WLTI.GGL.GSGLFV.SLTAF..
Retrocopy LVRGANLTHRQGMMVVGTDTSLAISSLLSLLLFTGMQM*IHQLAST*WLTIHGGLHGSGLFVLSLTAFKI

Parental  LENLVFGKGFQAKIFPEILLCLLLALFASGLIHRVCVTTCFIFSMIGLYYINKISSTLYQAAAPVLTPAK
          LENLVFGKG.QA..FPEILLCLLLALFASGLIHRVCVTTCFIFS.IGL.YINKI.STLYQAAA.VLT...
Retrocopy LENLVFGKGSQANTFPEILLCLLLALFASGLIHRVCVTTCFIFSVIGLCYINKI-STLYQAAAAVLTGPW

Parental  VTGKSKKR
          ....S..R
Retrocopy LLPRSQAR

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	25.63 RPM
SRP007412_cerebellum	0.00 RPM	15.52 RPM
SRP007412_heart	0.12 RPM	16.35 RPM
SRP007412_kidney	0.05 RPM	44.54 RPM
SRP007412_liver	0.03 RPM	37.64 RPM
SRP007412_testis	0.95 RPM	76.19 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1541 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1541 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2100
Gorilla gorilla	retro_ggor_1635
Pongo abelii	retro_pabe_1999
Macaca mulatta	retro_mmul_987
Callithrix jacchus	retro_cjac_1289

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011336	1 retrocopy	retro_amel_1789,
Canis familiaris	ENSCAFG00000017055	1 retrocopy	retro_cfam_1487,
Callithrix jacchus	ENSCJAG00000009017	1 retrocopy	retro_cjac_1289,
Felis catus	ENSFCAG00000025085	3 retrocopies	retro_fcat_1496, retro_fcat_477, retro_fcat_576,
Homo sapiens	ENSG00000163463	1 retrocopy	retro_hsap_2100,
Gorilla gorilla	ENSGGOG00000009303	1 retrocopy	retro_ggor_1635,
Macaca mulatta	ENSMMUG00000012180	2 retrocopies	retro_mmul_745, retro_mmul_987,
Mustela putorius furo	ENSMPUG00000005647	1 retrocopy	retro_mputfur_1653,
Nomascus leucogenys	ENSNLEG00000011864	1 retrocopy	retro_nleu_1306,
Oryctolagus cuniculus	ENSOCUG00000000347	1 retrocopy	retro_ocun_157,
Otolemur garnettii	ENSOGAG00000030271	1 retrocopy	retro_ogar_1306,
Pongo abelii	ENSPPYG00000000756	1 retrocopy	retro_pabe_1999,
Pan troglodytes	ENSPTRG00000001410	1 retrocopy	retro_ptro_1541 ,
Rattus norvegicus	ENSRNOG00000020542	1 retrocopy	retro_rnor_2128,
Ictidomys tridecemlineatus	ENSSTOG00000008829	1 retrocopy	retro_itri_1127,
Tarsius syrichta	ENSTSYG00000013228	2 retrocopies	retro_tsyr_1096, retro_tsyr_531,