RetrogeneDB ID: retro_pabe_3031

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6_random:6142702..6143128(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL42
• Ensembl ID: ENSPPYG00000004833
• Aliases: None
• Description: mitochondrial ribosomal protein L42 [Source:HGNC Symbol;Acc:14493]

Sequence

>retro_pabe_3031
ATGGCTGTGATTTTGTTACAATAGATGACAGTAAATCAAATTGTCTTGAATCATGTATTTCTATGCAAAATGGAGCTTTA
TACTGTGTGTGTTATAAATCTATGTATTCTTCTCTACCGGATGACTATAATTGCAAAAATAGAGCTTGCTGTGACTTCCA
ATGGCAGGACGTGAGCCTGCTACCAATCTCCTGTGGACATTCCCTATAAACACACAAAACCCATCCTTCAACCAGATCCT
GGGCACAATAATGAAGAAATACAAGATCAAGTGCTGAAAACCAGACTGGAAGAAAAAGGTGAACACCTTGAGCAAAGACC
CATGATAGACCAACTTAGCAAAATGTTCTTTAGTATTACACGCTGTTGGTATTCTCATGGACAGTATTAAAGATGTTGCA
AGAAACTAGATCTTCTAAAAGACAGA

Alignment

ORF - retro_pabe_3031 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVAAVKWVMSKRTILKHLF-PVQNGALYCVCHKSTYSPLPDDYNCS-VELAVTSDGRTIVCYHPSVDIP
          MAV............L.H.F...QNGALYCVC.KS.YS.LPDDYNC...ELAVTS.GRT..CY...VDIP
Retrocopy MAVILLQ*MTVNQIVLNHVF<SMQNGALYCVCYKSMYSSLPDDYNCK>IELAVTSNGRT*ACYQSPVDIP

Parental  YEHTKPIPRPDPVHNNEETHDQVLKTRLEEKVEHLEEGPMIEQLSKMFFTTKHRWYPHGRYHRCRKNLNP
          Y.HTKPI..PDP.HNNEE..DQVLKTRLEEK.EHLE..PMI.QLSKMFF.....WY.HG.Y.RC.K.L..
Retrocopy YKHTKPILQPDPGHNNEEIQDQVLKTRLEEKGEHLEQRPMIDQLSKMFFSITRCWYSHGQY*RCCKKLDL

Parental  PKDR
          .KDR
Retrocopy LKDR

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	11.89 RPM
SRP007412_cerebellum	0.00 RPM	28.21 RPM
SRP007412_heart	0.00 RPM	20.05 RPM
SRP007412_kidney	0.00 RPM	30.13 RPM
SRP007412_liver	0.00 RPM	11.78 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3031 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3031 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3031 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009832	1 retrocopy	retro_amel_403,
Bos taurus	ENSBTAG00000002708	3 retrocopies	retro_btau_1395, retro_btau_346, retro_btau_775,
Callithrix jacchus	ENSCJAG00000032825	4 retrocopies	retro_cjac_1541, retro_cjac_3684, retro_cjac_3966, retro_cjac_722,
Homo sapiens	ENSG00000198015	3 retrocopies	retro_hsap_3427, retro_hsap_3528, retro_hsap_3844,
Gorilla gorilla	ENSGGOG00000022760	5 retrocopies	retro_ggor_1983, retro_ggor_2317, retro_ggor_2385, retro_ggor_2483, retro_ggor_2589,
Loxodonta africana	ENSLAFG00000013779	1 retrocopy	retro_lafr_681,
Macaca mulatta	ENSMMUG00000016805	3 retrocopies	retro_mmul_1751, retro_mmul_1850, retro_mmul_2210,
Nomascus leucogenys	ENSNLEG00000005699	5 retrocopies	retro_nleu_1364, retro_nleu_1724, retro_nleu_1979, retro_nleu_493, retro_nleu_606,
Oryctolagus cuniculus	ENSOCUG00000010928	7 retrocopies	retro_ocun_1321, retro_ocun_1378, retro_ocun_1497, retro_ocun_1716, retro_ocun_1717, retro_ocun_622, retro_ocun_686,
Ochotona princeps	ENSOPRG00000010967	5 retrocopies	retro_opri_190, retro_opri_51, retro_opri_653, retro_opri_747, retro_opri_997,
Procavia capensis	ENSPCAG00000003791	1 retrocopy	retro_pcap_179,
Pongo abelii	ENSPPYG00000004833	7 retrocopies	retro_pabe_1286, retro_pabe_2368, retro_pabe_2840, retro_pabe_2914, retro_pabe_3031 , retro_pabe_3054, retro_pabe_3552,
Pan troglodytes	ENSPTRG00000022791	3 retrocopies	retro_ptro_1046, retro_ptro_2327, retro_ptro_2396,
Rattus norvegicus	ENSRNOG00000042740	4 retrocopies	retro_rnor_1383, retro_rnor_633, retro_rnor_729, retro_rnor_920,
Sus scrofa	ENSSSCG00000030478	4 retrocopies	retro_sscr_504, retro_sscr_505, retro_sscr_912, retro_sscr_946,
Ictidomys tridecemlineatus	ENSSTOG00000026544	12 retrocopies	retro_itri_1020, retro_itri_1132, retro_itri_1266, retro_itri_1285, retro_itri_1353, retro_itri_1695, retro_itri_1793, retro_itri_268, retro_itri_284, retro_itri_393, retro_itri_558, retro_itri_899,
Tarsius syrichta	ENSTSYG00000006370	3 retrocopies	retro_tsyr_1296, retro_tsyr_2113, retro_tsyr_276,
Tursiops truncatus	ENSTTRG00000003312	2 retrocopies	retro_ttru_1632, retro_ttru_416,
Vicugna pacos	ENSVPAG00000007658	1 retrocopy	retro_vpac_336,