RetrogeneDB ID: retro_pabe_2028

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a_random:1792044..1792283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7B
• Ensembl ID: ENSPPYG00000020494
• Aliases: None
• Description: Cytochrome c oxidase subunit 7B, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5R9K2]

Sequence

>retro_pabe_2028
ATGTTTCACTGGTCAAAAAATGCACTATGTCATCTCCAAGATCAAAGCATTCAGCAAACAATGGCAAGGCAGAGCCACCA
GAAAAGTTCACCTGATTTTCATGACAATACGATAATGCTGTATTAGATAGTGGAGCCACTTTCTGTATTGCTATATGGAC
ATATGTAGCAACACAAATCAGAATAGAATGGAACCTGGACCCTGCTGGCAGAGTCACCCCAAAGGAATGGAGAGATCAG

Alignment

ORF - retro_pabe_2028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFPLVKNALNRLQVRSIQQTMARQSHQKRTPDFHD-KYGNAVLASGATFCIVTWTYVATQVGIEWNLSPV
          MF...KNAL..LQ..SIQQTMARQSHQK..PDFHD..Y.NAVL.SGATFCI..WTYVATQ..IEWNL.P.
Retrocopy MFHWSKNALCHLQDQSIQQTMARQSHQKSSPDFHD<QYDNAVLDSGATFCIAIWTYVATQIRIEWNLDPA

Parental  GRVTPKEWRNQ
          GRVTPKEWR.Q
Retrocopy GRVTPKEWRDQ

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	35.28 RPM
SRP007412_cerebellum	0.00 RPM	65.66 RPM
SRP007412_heart	0.00 RPM	213.64 RPM
SRP007412_kidney	0.00 RPM	74.08 RPM
SRP007412_liver	0.00 RPM	45.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2028 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2028 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006153	6 retrocopies	retro_amel_25, retro_amel_313, retro_amel_459, retro_amel_484, retro_amel_669, retro_amel_807,
Bos taurus	ENSBTAG00000047768	3 retrocopies	retro_btau_214, retro_btau_22, retro_btau_59,
Callithrix jacchus	ENSCJAG00000004045	5 retrocopies	retro_cjac_2496, retro_cjac_2716, retro_cjac_345, retro_cjac_844, retro_cjac_973,
Cavia porcellus	ENSCPOG00000014781	2 retrocopies	retro_cpor_117, retro_cpor_252,
Echinops telfairi	ENSETEG00000016695	9 retrocopies	retro_etel_1049, retro_etel_1180, retro_etel_1651, retro_etel_1736, retro_etel_1805, retro_etel_2057, retro_etel_59, retro_etel_860, retro_etel_910,
Felis catus	ENSFCAG00000023091	2 retrocopies	retro_fcat_534, retro_fcat_590,
Homo sapiens	ENSG00000131174	4 retrocopies	retro_hsap_157, retro_hsap_16, retro_hsap_2305, retro_hsap_920,
Gorilla gorilla	ENSGGOG00000023347	9 retrocopies	retro_ggor_1539, retro_ggor_1617, retro_ggor_1634, retro_ggor_1707, retro_ggor_1779, retro_ggor_245, retro_ggor_443, retro_ggor_52, retro_ggor_579,
Loxodonta africana	ENSLAFG00000022996	4 retrocopies	retro_lafr_27, retro_lafr_555, retro_lafr_716, retro_lafr_927,
Microcebus murinus	ENSMICG00000014521	3 retrocopies	retro_mmur_256, retro_mmur_379, retro_mmur_56,
Myotis lucifugus	ENSMLUG00000022443	3 retrocopies	retro_mluc_1491, retro_mluc_2521, retro_mluc_277,
Macaca mulatta	ENSMMUG00000015861	5 retrocopies	retro_mmul_1120, retro_mmul_1941, retro_mmul_2400, retro_mmul_571, retro_mmul_800,
Mus musculus	ENSMUSG00000031231	5 retrocopies	retro_mmus_195, retro_mmus_2062, retro_mmus_2157, retro_mmus_2731, retro_mmus_502,
Pongo abelii	ENSPPYG00000020494	18 retrocopies	retro_pabe_1824, retro_pabe_1904, retro_pabe_2016, retro_pabe_2017, retro_pabe_2025, retro_pabe_2026, retro_pabe_2028 , retro_pabe_2029, retro_pabe_2030, retro_pabe_2034, retro_pabe_2038, retro_pabe_2121, retro_pabe_22, retro_pabe_270, retro_pabe_465, retro_pabe_587, retro_pabe_793, retro_pabe_836,
Pan troglodytes	ENSPTRG00000022049	9 retrocopies	retro_ptro_12, retro_ptro_1431, retro_ptro_1510, retro_ptro_153, retro_ptro_1629, retro_ptro_1714, retro_ptro_3014, retro_ptro_349, retro_ptro_760,
Pteropus vampyrus	ENSPVAG00000003237	2 retrocopies	retro_pvam_1, retro_pvam_1234,
Rattus norvegicus	ENSRNOG00000028451	5 retrocopies	retro_rnor_2351, retro_rnor_2387, retro_rnor_2959, retro_rnor_763, retro_rnor_999,
Sus scrofa	ENSSSCG00000030970	2 retrocopies	retro_sscr_938, retro_sscr_991,
Tursiops truncatus	ENSTTRG00000004387	3 retrocopies	retro_ttru_1097, retro_ttru_556, retro_ttru_7,
Vicugna pacos	ENSVPAG00000001324	2 retrocopies	retro_vpac_7, retro_vpac_87,