RetrogeneDB ID: retro_ptro_1981

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:46624787..46625251(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C18ORF21
• Ensembl ID: ENSPTRG00000009973
• Aliases: None
• Description: Chromosome 18 open reading frame 21 [Source:UniProtKB/TrEMBL;Acc:K7CUG3]

Sequence

>retro_ptro_1981
GATAAGAGTACTTTTGAAGAAACGTGTCCACACTGTTTGCAGTTGCTGATTCTGGATAACTCTTGAGTGTGTCTCAAACC
CAAAGCCACATTGACACCCAAAATACAGAAACTGATTAATCGAGAAGCATGAAATTATACACTCAGTTTTAAAGAAGCAA
AAATTGTGAAAAAATTCAAAGACGACAAAAGTGTATTGTTGATTACTTGTAAAACATGCCGCAGAACAGTGAAACATCAT
GGTAAGAGTAGAAGCTTTCTATCAGCATTGAAGAGCAATCCTACTACTCCTCAAGTAAACTCAGCCTGAAGACACCAAAG
AGAAGGACTGCAAACCCAAATCATGAGATGTCTGGTTCCAAAGGCAAAAGCCCAGTATTGATTTCCAGAACACCTACATC
TGGAGAGTCAGTATTTTCTTGCTCCCCAAAGAATGTGAGCAAAACAAAGAAACATTTCCCTCAA

Alignment

ORF - retro_ptro_1981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.69 %
• Parental protein coverage: 70.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DKSTFEETCPYCFQLLVLDNSRVRLKPKAKLTPKIQKLLNREARNYTLSFKEAKMVKKFKDSKSVLLITC
          DKSTFEETCP.C.QLL.LDNS.V.LKPKA.LTPKIQKL.NREA.NYTLSFKEAK.VKKFKD.KSVLLITC
Retrocopy DKSTFEETCPHCLQLLILDNS*VCLKPKATLTPKIQKLINREA*NYTLSFKEAKIVKKFKDDKSVLLITC

Parental  KTCNRTVKHHGKSRSFLSTLKSNPATP-TSKLSLKTPERRTANPNHDMSGSKGKSPASVFRTPTSGQSVS
          KTC.RTVKHHGKSRSFLS.LKSNP.TP..SKLSLKTP.RRTANPNH.MSGSKGKSP....RTPTSG.SV.
Retrocopy KTCRRTVKHHGKSRSFLSALKSNPTTP<SSKLSLKTPKRRTANPNHEMSGSKGKSPVLISRTPTSGESVF

Parental  TCSSKNTSKTKKHFSQ
          .CS.KN.SKTKKHF.Q
Retrocopy SCSPKNVSKTKKHFPQ

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	5.84 RPM
SRP007412_cerebellum	0.00 RPM	7.21 RPM
SRP007412_heart	0.00 RPM	5.10 RPM
SRP007412_kidney	0.00 RPM	9.41 RPM
SRP007412_liver	0.00 RPM	8.12 RPM
SRP007412_testis	0.00 RPM	31.83 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1981 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1981 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3062
Gorilla gorilla	retro_ggor_2102
Pongo abelii	retro_pabe_2536
Macaca mulatta	retro_mmul_1876
Callithrix jacchus	retro_cjac_2169

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029548	1 retrocopy	retro_cfam_1636,
Callithrix jacchus	ENSCJAG00000021041	2 retrocopies	retro_cjac_1030, retro_cjac_2169,
Cavia porcellus	ENSCPOG00000025449	1 retrocopy	retro_cpor_1461,
Felis catus	ENSFCAG00000000626	1 retrocopy	retro_fcat_1717,
Homo sapiens	ENSG00000141428	1 retrocopy	retro_hsap_3062,
Gorilla gorilla	ENSGGOG00000026334	1 retrocopy	retro_ggor_2102,
Macaca mulatta	ENSMMUG00000018782	1 retrocopy	retro_mmul_1876,
Monodelphis domestica	ENSMODG00000025605	1 retrocopy	retro_mdom_260,
Mus musculus	ENSMUSG00000024273	2 retrocopies	retro_mmus_1676, retro_mmus_610,
Nomascus leucogenys	ENSNLEG00000006237	1 retrocopy	retro_nleu_1655,
Oryctolagus cuniculus	ENSOCUG00000028046	2 retrocopies	retro_ocun_1910, retro_ocun_435,
Ochotona princeps	ENSOPRG00000011163	2 retrocopies	retro_opri_1222, retro_opri_283,
Pongo abelii	ENSPPYG00000009110	1 retrocopy	retro_pabe_2536,
Pan troglodytes	ENSPTRG00000009973	2 retrocopies	retro_ptro_1981 , retro_ptro_2935,
Pteropus vampyrus	ENSPVAG00000009174	3 retrocopies	retro_pvam_1086, retro_pvam_1488, retro_pvam_629,
Tupaia belangeri	ENSTBEG00000016670	1 retrocopy	retro_tbel_4056,
Tarsius syrichta	ENSTSYG00000010817	2 retrocopies	retro_tsyr_1675, retro_tsyr_1787,