RetrogeneDB ID: retro_pabe_612

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:86493276..86493734(-)
• Located in intron of: ENSPPYG00000002448

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSPPYG00000001736
• Aliases: None
• Description: 60S ribosomal protein L11 [Source:RefSeq peptide;Acc:NP_001125385]

Sequence

>retro_pabe_612
GTGGTGCAGGATCAAGGTGAAAAGGATAACCCCGTGCAGAATTTTGCATCTGCAGGCTCTGCTTCAATATCTGTTTAGGA
GAAAGTGGAGACAGACTGACCTGAGTAACCAAGGCGTTGGAGCAGCTTATAGGTCAGAACCACGTGTTTTCCAAAGCTAG
ATATACTGTTAGTCCCTTTGGCAACAGAAGAAATGAAAAGACTGTTTGCTGCACAGTTCGAGGGGCCAAGGCAGACGAAA
TCCTGGAGAATGATCTATAGGTGCAGGAGCGTGAGTTAAGAAAAAATAACTTCTCAGATACTGGAAACTTTGGTTTTGGG
ACCCAGGAACACATTGATCTGGGTATCAGATATGACCCAAGCATTGATGTCTACAGCCTGGACTTCTATGTGGTGCTGGA
AAAGCCAGGTTTCATCATTGCAGGTAAGAAGCGCAGGACAGGCTTCAATGGTGCCAAA

Alignment

ORF - retro_pabe_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.9 %
• Parental protein coverage: 86.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQDQGEKENPMR-ELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKIA
          ..QDQGEK.NP...E..I..LC.NIC.GESGDRLT...K.LEQL.GQ..VFSKARYTV..FG.RRNEK..
Retrocopy VVQDQGEKDNPVQ<EFCICRLCFNICLGESGDRLT*VTKALEQLIGQNHVFSKARYTVSPFGNRRNEK-T

Parental  VHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGF
          V.CTVRGAKA.EILE..L.V.E.ELRKNNFSDTGNFGFG.QEHIDLGI.YDPSI..Y.LDFYVVL..PGF
Retrocopy VCCTVRGAKADEILENDL*VQERELRKNNFSDTGNFGFGTQEHIDLGIRYDPSIDVYSLDFYVVLEKPGF

Parental  SIADKKRRTGCIGAK
          .IA.KKRRTG..GAK
Retrocopy IIAGKKRRTGFNGAK

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	0.11 RPM	192.85 RPM
SRP007412_cerebellum	1.34 RPM	179.24 RPM
SRP007412_heart	0.15 RPM	198.35 RPM
SRP007412_kidney	0.30 RPM	581.36 RPM
SRP007412_liver	0.31 RPM	455.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_612 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_612 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_606
Gorilla gorilla	retro_ggor_533
Macaca mulatta	retro_mmul_2415

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020905	1 retrocopy	retro_btau_267,
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Callithrix jacchus	ENSCJAG00000020953	1 retrocopy	retro_cjac_790,
Dasypus novemcinctus	ENSDNOG00000011230	2 retrocopies	retro_dnov_1453, retro_dnov_605,
Homo sapiens	ENSG00000142676	6 retrocopies	retro_hsap_1159, retro_hsap_1801, retro_hsap_2272, retro_hsap_3238, retro_hsap_606, retro_hsap_712,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Loxodonta africana	ENSLAFG00000030853	2 retrocopies	retro_lafr_371, retro_lafr_434,
Macropus eugenii	ENSMEUG00000013738	3 retrocopies	retro_meug_488, retro_meug_517, retro_meug_633,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica	ENSMODG00000012828	1 retrocopy	retro_mdom_641,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus	ENSOANG00000000321	1 retrocopy	retro_oana_49,
Oryctolagus cuniculus	ENSOCUG00000022928	1 retrocopy	retro_ocun_1387,
Pongo abelii	ENSPPYG00000001736	6 retrocopies	retro_pabe_1478, retro_pabe_1946, retro_pabe_2686, retro_pabe_612 , retro_pabe_615, retro_pabe_964,
Pteropus vampyrus	ENSPVAG00000004282	1 retrocopy	retro_pvam_1068,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Sus scrofa	ENSSSCG00000024260	4 retrocopies	retro_sscr_1048, retro_sscr_1049, retro_sscr_1074, retro_sscr_819,
Tarsius syrichta	ENSTSYG00000001349	6 retrocopies	retro_tsyr_1138, retro_tsyr_127, retro_tsyr_1583, retro_tsyr_1605, retro_tsyr_516, retro_tsyr_520,