RetrogeneDB ID: retro_ptro_461

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:118085193..118085629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOMM22
• Ensembl ID: ENSPTRG00000014374
• Aliases: None
• Description: None

Sequence

>retro_ptro_461
ATAGCTGTCACCATGGCTGCTGTCGGTGCAGGGGAACCCCCATCCCCAGATGTCCCCGGATGAATTGCTCCCAAAAGGCA
AAGCTGTGAAGACTGAGGAGGAGCTGGAGGAGGATGATGATGAGGAGCTAGAGGAGACCCTGTCAGAGAGACTATGGGGC
CTGACGGAGATGTTTCTGGAGAGGGTCCGGTCCGTGGCTGGAGCCACTTCTGATCTCTTCCTCTTTGTGGCTCAAAAAAT
GTACAGGTTTTCCAGGGCAGCCTTGTGGACTGGGACCACTTCCTTTATGATCCTGGTTCTTCCCCTTGTCTTTGAGACTG
AGAAGTTGCAAATGGAGCAACAGCAGCAACTGCAGCAGCAGCAGATACTTCTAGGGCCTAACACAGGGCTCTCAGGAGGA
ATGCCAGGGGCTCTACCTTCACTTCCTGGAAAGATC

Alignment

ORF - retro_ptro_461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAVAAAGA-GEPQ---SPDELLPKGDAEKPEEELEEDDDEELDETLSERLWGLTEMFPERVRSAAGAT
          .A...AA.GA.G.P....SPDELLPKG.A.K.EEELEEDDDEEL.ETLSERLWGLTEMF.ERVRS.AGAT
Retrocopy IAVTMAAVGA>GNPHPQMSPDELLPKGKAVKTEEELEEDDDEELEETLSERLWGLTEMFLERVRSVAGAT

Parental  FDLSLFVAQKMYRFSRAALWIGTTSFMILVLPVVFETEKLQMEQQQQLQQRQILLGPNTGLSGGMPGALP
          .DL.LFVAQKMYRFSRAALW.GTTSFMILVLP.VFETEK.............ILLGPNTGLSGGMPGALP
Retrocopy SDLFLFVAQKMYRFSRAALWTGTTSFMILVLPLVFETEKXXXXXXXXXXXXXILLGPNTGLSGGMPGALP

Parental  SLPGKI
          SLPGKI
Retrocopy SLPGKI

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	36.50 RPM
SRP007412_cerebellum	0.00 RPM	19.39 RPM
SRP007412_heart	0.00 RPM	22.27 RPM
SRP007412_kidney	0.03 RPM	30.05 RPM
SRP007412_liver	0.03 RPM	27.17 RPM
SRP007412_testis	0.00 RPM	54.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_461 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_461 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_633
Gorilla gorilla	retro_ggor_554
Pongo abelii	retro_pabe_563
Macaca mulatta	retro_mmul_2426

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010692	3 retrocopies	retro_amel_542, retro_amel_58, retro_amel_867,
Canis familiaris	ENSCAFG00000001383	2 retrocopies	retro_cfam_1817, retro_cfam_197,
Callithrix jacchus	ENSCJAG00000011731	5 retrocopies	retro_cjac_1220, retro_cjac_1230, retro_cjac_3675, retro_cjac_498, retro_cjac_94,
Cavia porcellus	ENSCPOG00000005963	1 retrocopy	retro_cpor_754,
Equus caballus	ENSECAG00000010359	1 retrocopy	retro_ecab_334,
Erinaceus europaeus	ENSEEUG00000006428	1 retrocopy	retro_eeur_29,
Echinops telfairi	ENSETEG00000000544	7 retrocopies	retro_etel_123, retro_etel_1477, retro_etel_154, retro_etel_1753, retro_etel_190, retro_etel_2025, retro_etel_599,
Homo sapiens	ENSG00000100216	6 retrocopies	retro_hsap_1249, retro_hsap_2875, retro_hsap_3003, retro_hsap_4928, retro_hsap_633, retro_hsap_907,
Gorilla gorilla	ENSGGOG00000013230	4 retrocopies	retro_ggor_3084, retro_ggor_554, retro_ggor_734, retro_ggor_980,
Macropus eugenii	ENSMEUG00000002901	1 retrocopy	retro_meug_855,
Microcebus murinus	ENSMICG00000011792	3 retrocopies	retro_mmur_1549, retro_mmur_408, retro_mmur_892,
Myotis lucifugus	ENSMLUG00000003761	2 retrocopies	retro_mluc_2116, retro_mluc_543,
Macaca mulatta	ENSMMUG00000000364	8 retrocopies	retro_mmul_1020, retro_mmul_1113, retro_mmul_1459, retro_mmul_241, retro_mmul_2426, retro_mmul_2438, retro_mmul_2532, retro_mmul_498,
Mustela putorius furo	ENSMPUG00000013156	2 retrocopies	retro_mputfur_1038, retro_mputfur_1254,
Mus musculus	ENSMUSG00000022427	2 retrocopies	retro_mmus_1884, retro_mmus_2496,
Nomascus leucogenys	ENSNLEG00000015159	6 retrocopies	retro_nleu_2116, retro_nleu_2142, retro_nleu_2249, retro_nleu_375, retro_nleu_454, retro_nleu_617,
Otolemur garnettii	ENSOGAG00000029583	9 retrocopies	retro_ogar_1153, retro_ogar_1294, retro_ogar_1905, retro_ogar_2022, retro_ogar_2067, retro_ogar_214, retro_ogar_3111, retro_ogar_3328, retro_ogar_792,
Pongo abelii	ENSPPYG00000011825	6 retrocopies	retro_pabe_1041, retro_pabe_1088, retro_pabe_1968, retro_pabe_2489, retro_pabe_563, retro_pabe_782,
Pan troglodytes	ENSPTRG00000014374	6 retrocopies	retro_ptro_1583, retro_ptro_2031, retro_ptro_2117, retro_ptro_461 , retro_ptro_627, retro_ptro_860,
Rattus norvegicus	ENSRNOG00000014058	4 retrocopies	retro_rnor_1323, retro_rnor_2280, retro_rnor_548, retro_rnor_549,
Sus scrofa	ENSSSCG00000000097	1 retrocopy	retro_sscr_310,
Tupaia belangeri	ENSTBEG00000015683	4 retrocopies	retro_tbel_1810, retro_tbel_2901, retro_tbel_2922, retro_tbel_3041,
Vicugna pacos	ENSVPAG00000001485	1 retrocopy	retro_vpac_586,