RetrogeneDB ID: retro_ptro_34

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:199415649..199416099(+)
• Located in intron of: ENSPTRG00000001999

Retrocopy information

• Ensembl ID: ENSPTRG00000041434
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: OSTC
• Ensembl ID: ENSPTRG00000024222
• Aliases: None
• Description: oligosaccharyltransferase complex subunit (non-catalytic) [Source:HGNC Symbol;Acc:24448]

Sequence

>retro_ptro_34
ATGGAGACTTTGTACCGTGTCCCGTTCTTAGTGCTCGAATGTCCCAACCTGAAGCTGAAGAAGCCGCCCTGGTTGCACAT
GCCGTCGGCCATGACTGTGTATGCTCTGGTGGTGGTGTCTTACTTCCTCATCACCGGAGGAATAATTTATGATGTTATTG
TTGAACCTCCAAGTGTCGGTTCTATGACTGATGAACATGGACATCAGAGGCCAGTAGCTTTCTTGGCCTACAGAGTAAAT
GGACAATATATTATGGAAGGACTTGCATCCAGCTTCCTATTTACAATGGGAGGTTTAGGTTTCATAATCCTGGACCGATC
GAATGCACCAAATATCCCAAAACTCAATAGATTCCTTCTTCTGTTCATTGGATTCGTCTGTGTCCTATTGAGTTTTTTCA
TGGCTAGAGTATTCATGAGAATGAAACTGCCGGGCTATCTGATGGGTTAG

Alignment

ORF - retro_ptro_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 84.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METLYRVPFLVLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQR
          METLYRVPFLVLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQR
Retrocopy METLYRVPFLVLECPNLKLKKPPWLHMPSAMTVYALVVVSYFLITGGIIYDVIVEPPSVGSMTDEHGHQR

Parental  PVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLLSFFMARVFMR
          PVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLLSFFMARVFMR
Retrocopy PVAFLAYRVNGQYIMEGLASSFLFTMGGLGFIILDRSNAPNIPKLNRFLLLFIGFVCVLLSFFMARVFMR

Parental  MKLP
          MKLP
Retrocopy MKLP

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	0.45 RPM	1.64 RPM
SRP007412_cerebellum	0.07 RPM	0.65 RPM
SRP007412_heart	0.23 RPM	0.76 RPM
SRP007412_kidney	0.89 RPM	2.01 RPM
SRP007412_liver	0.85 RPM	3.96 RPM
SRP007412_testis	0.21 RPM	1.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_34 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_34 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_34 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011611	1 retrocopy	retro_btau_753,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Dasypus novemcinctus	ENSDNOG00000011172	2 retrocopies	retro_dnov_12, retro_dnov_1973,
Homo sapiens	ENSG00000198856	7 retrocopies	retro_hsap_1746, retro_hsap_2013, retro_hsap_2972, retro_hsap_3598, retro_hsap_3686, retro_hsap_376, retro_hsap_4246,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Loxodonta africana	ENSLAFG00000026381	7 retrocopies	retro_lafr_1046, retro_lafr_17, retro_lafr_222, retro_lafr_231, retro_lafr_444, retro_lafr_549, retro_lafr_618,
Myotis lucifugus	ENSMLUG00000000478	2 retrocopies	retro_mluc_1366, retro_mluc_1511,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Nomascus leucogenys	ENSNLEG00000012929	11 retrocopies	retro_nleu_1372, retro_nleu_1436, retro_nleu_2026, retro_nleu_2265, retro_nleu_2274, retro_nleu_2665, retro_nleu_2796, retro_nleu_2826, retro_nleu_297, retro_nleu_474, retro_nleu_923,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Otolemur garnettii	ENSOGAG00000033684	1 retrocopy	retro_ogar_578,
Pan troglodytes	ENSPTRG00000024222	1 retrocopy	retro_ptro_34 ,
Tursiops truncatus	ENSTTRG00000003446	1 retrocopy	retro_ttru_582,