RetrogeneDB ID: retro_pabe_3012

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:142417493..142418036(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5F1
• Ensembl ID: ENSPPYG00000001032
• Aliases: None
• Description: ATP synthase subunit b, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001124636]

Sequence

>retro_pabe_3012
ATGCTGTCCCAGGTGGCACATTCTGCCACCACCGTGGTGGCCTCCTCTCTGAAGAATACAGCCTTCATACGTCCAGGGAT
ATCGCAGGCAACAAAGACCTTTCACACAGGGCAGCCATGCCTTGCCCTTCTGCCACCTCTTCCTGAATATGGAGGGAAAG
TTCATTTGGGGCTGATCCCTGAGGAATTCTTCCAGTTTCTTTATCCTAGAACCGGTGTAACAGGACCCTATGTGCTCAGA
ACTGGGCTTATCTTGTATGGTTTATCCAAAGAAATATATATGATTACCCCAGAGACCTTGTCTACCACATCAATAGTATG
GTTACTTGTCCAAATAATTTTAAAATATGGTGCCTCTATTGGAGATTTTGCTGAAAAATTCAATGAGCAAAAAATTGCCC
AACTAGAAGAGGTGAAGCAGGCTTCTATCAGACAAATCCAGGATGCAACTGATTTGGAGAAGTCACAGCAGGCACTCGTT
CAGAAGCACCATTACCTTTTTGATGTGCAGAAAAACAACATTGCTATGGCTTTGGAGGTTACT

Alignment

ORF - retro_pabe_3012 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.72 %
• Parental protein coverage: 70.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSRVVLSAAATAAPSLKNAAFLGPGVLQATRTFHTGPPHLAPVPPLPEYGGKVRYGLIPEEFFQFLYPK
          MLS.V..SA....A.SLKN.AF..PG..QAT.TFHTG.P.LA..PPLPEYGGKV..GLIPEEFFQFLYP.
Retrocopy MLSQVAHSATTVVASSLKNTAFIRPGISQATKTFHTGQPCLALLPPLPEYGGKVHLGLIPEEFFQFLYPR

Parental  TGVTGPYVLGTGLILYALSKEIYVISAETFTALSLIGVMVYGIKKYGPAVADFADKLNEQKLAQLEEAKQ
          TGVTGPYVL.TGLILY.LSKEIY.I..ET....S.....V..I.KYG....DFA.K.NEQK.AQLEE.KQ
Retrocopy TGVTGPYVLRTGLILYGLSKEIYMITPETLSTTSIVWLLVQIILKYGASIGDFAEKFNEQKIAQLEEVKQ

Parental  TSIQQIQNAIDMEKSQQALVQKRHYLFDVQRNNIAMALEVT
          .SI.QIQ.A.D.EKSQQALVQK.HYLFDVQ.NNIAMALEVT
Retrocopy ASIRQIQDATDLEKSQQALVQKHHYLFDVQKNNIAMALEVT

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	63.42 RPM
SRP007412_cerebellum	0.00 RPM	84.27 RPM
SRP007412_heart	0.00 RPM	152.71 RPM
SRP007412_kidney	0.00 RPM	108.69 RPM
SRP007412_liver	0.00 RPM	60.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3012 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3012 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3673
Gorilla gorilla	retro_ggor_2482
Macaca mulatta	retro_mmul_1791
Callithrix jacchus	retro_cjac_2482

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005433	1 retrocopy	retro_amel_1118,
Bos taurus	ENSBTAG00000006441	1 retrocopy	retro_btau_745,
Callithrix jacchus	ENSCJAG00000013353	9 retrocopies	retro_cjac_1943, retro_cjac_2270, retro_cjac_2482, retro_cjac_2747, retro_cjac_2815, retro_cjac_2854, retro_cjac_3067, retro_cjac_528, retro_cjac_833,
Cavia porcellus	ENSCPOG00000014070	3 retrocopies	retro_cpor_1120, retro_cpor_448, retro_cpor_563,
Equus caballus	ENSECAG00000018599	1 retrocopy	retro_ecab_494,
Echinops telfairi	ENSETEG00000010713	3 retrocopies	retro_etel_105, retro_etel_1784, retro_etel_408,
Felis catus	ENSFCAG00000028321	1 retrocopy	retro_fcat_1012,
Homo sapiens	ENSG00000116459	6 retrocopies	retro_hsap_1705, retro_hsap_1951, retro_hsap_3673, retro_hsap_3762, retro_hsap_3812, retro_hsap_828,
Gorilla gorilla	ENSGGOG00000005215	6 retrocopies	retro_ggor_1279, retro_ggor_1721, retro_ggor_2482, retro_ggor_2530, retro_ggor_2564, retro_ggor_678,
Loxodonta africana	ENSLAFG00000004809	1 retrocopy	retro_lafr_602,
Microcebus murinus	ENSMICG00000011992	1 retrocopy	retro_mmur_846,
Myotis lucifugus	ENSMLUG00000012417	1 retrocopy	retro_mluc_2184,
Macaca mulatta	ENSMMUG00000003313	3 retrocopies	retro_mmul_1086, retro_mmul_1659, retro_mmul_1791,
Mus musculus	ENSMUSG00000000563	2 retrocopies	retro_mmus_2215, retro_mmus_791,
Nomascus leucogenys	ENSNLEG00000003971	8 retrocopies	retro_nleu_172, retro_nleu_2090, retro_nleu_2153, retro_nleu_2154, retro_nleu_2546, retro_nleu_260, retro_nleu_524, retro_nleu_975,
Oryctolagus cuniculus	ENSOCUG00000007809	1 retrocopy	retro_ocun_25,
Otolemur garnettii	ENSOGAG00000011486	3 retrocopies	retro_ogar_2102, retro_ogar_2295, retro_ogar_2887,
Pongo abelii	ENSPPYG00000001032	3 retrocopies	retro_pabe_2056, retro_pabe_3012 , retro_pabe_3111,
Pan troglodytes	ENSPTRG00000001099	5 retrocopies	retro_ptro_1154, retro_ptro_1305, retro_ptro_2553, retro_ptro_2586, retro_ptro_578,
Pteropus vampyrus	ENSPVAG00000010604	3 retrocopies	retro_pvam_1061, retro_pvam_1110, retro_pvam_283,
Sorex araneus	ENSSARG00000002107	3 retrocopies	retro_sara_424, retro_sara_428, retro_sara_610,
Sarcophilus harrisii	ENSSHAG00000013185	1 retrocopy	retro_shar_700,
Ictidomys tridecemlineatus	ENSSTOG00000007630	3 retrocopies	retro_itri_1146, retro_itri_1219, retro_itri_503,
Tarsius syrichta	ENSTSYG00000000420	5 retrocopies	retro_tsyr_1226, retro_tsyr_1553, retro_tsyr_1852, retro_tsyr_502, retro_tsyr_511,
Tursiops truncatus	ENSTTRG00000001546	1 retrocopy	retro_ttru_1654,
Vicugna pacos	ENSVPAG00000000206	2 retrocopies	retro_vpac_154, retro_vpac_319,