RetrogeneDB ID: retro_pabe_2536

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:86983986..86984450(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C18orf21
• Ensembl ID: ENSPPYG00000009110
• Aliases: None
• Description: chromosome 18 open reading frame 21 [Source:HGNC Symbol;Acc:28802]

Sequence

>retro_pabe_2536
GATAAGAGTACTTTTGAAGAAACGTGTCCACACTGTTTGCAGTTGCTGATTCTGGATAACTCTTGAGTGTGTCTCAAACC
CAAAGCCATAATGACACCCAAAATACAGAAACTGATTAATCAAGAAGCATGAAATTATACACTCAGTTTTAAAGAAGCAA
AAATTGTGAAAAAGTTCAAAGACTACAAAAGTGTATTGTTGATTACTTGTAAAACATGCCACAGAACAGTGAAACATCAT
GGTAAGAGTAGAAGCTTTCTATCAGCATTGAAGAACAATCCTACTACTCCTCAAGTAAACTCAGCCTGAAGACACTAAAG
AGAAGGACTGCAAACCCAAATCATGAGATGTCTTGTTCCAAAGGCAAGAGCCCAGTATTGACTTTCAGAACACCTGCATC
TGGAGAGTCAGTATTTTCTTGCTCCTCAAAGAATGTGAGCAAAACAAAGAAAGATTTCCCTCAA

Alignment

ORF - retro_pabe_2536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.49 %
• Parental protein coverage: 71.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DKSTFEETCPYCFQLLVLDNSRVRLKPKAKLTPKIQKLLNREARNYTLSFKEAKIVKKFKDSKSVLLITC
          DKSTFEETCP.C.QLL.LDNS.V.LKPKA..TPKIQKL.N.EA.NYTLSFKEAKIVKKFKD.KSVLLITC
Retrocopy DKSTFEETCPHCLQLLILDNS*VCLKPKAIMTPKIQKLINQEA*NYTLSFKEAKIVKKFKDYKSVLLITC

Parental  KTCNRTVKHHGKSRSFLSTLKSNPATP-TSKLSLTTPERRTANPNHDMSGSKGKSPASIFRTPTSGQSVS
          KTC.RTVKHHGKSRSFLS.LK.NP.TP..SKLSL.T..RRTANPNH.MS.SKGKSP...FRTP.SG.SV.
Retrocopy KTCHRTVKHHGKSRSFLSALKNNPTTP<SSKLSLKTLKRRTANPNHEMSCSKGKSPVLTFRTPASGESVF

Parental  TCSSKNTSKTKKHFSQ
          .CSSKN.SKTKK.F.Q
Retrocopy SCSSKNVSKTKKDFPQ

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	0.06 RPM	6.08 RPM
SRP007412_cerebellum	0.12 RPM	9.61 RPM
SRP007412_heart	0.06 RPM	3.49 RPM
SRP007412_kidney	0.03 RPM	5.47 RPM
SRP007412_liver	0.00 RPM	4.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2536 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2536 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2536 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3062
Pan troglodytes	retro_ptro_1981
Gorilla gorilla	retro_ggor_2102
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,