RetrogeneDB ID: retro_pabe_520

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:50465080..50465556(+)
• Located in intron of: ENSPPYG00000002274

Retrocopy information

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

Parental gene information

• Parental gene symbol: CACYBP
• Ensembl ID: ENSPPYG00000000486
• Aliases: None
• Description: calcyclin-binding protein [Source:RefSeq peptide;Acc:NP_001127554]

Sequence

>retro_pabe_520
GCTTTGGAAGAGCTACAGAAACATCTAGAAGAAGCAAAGGTGTTGCTGGTGAAGGCTACTAGGAAAGGAGTACGCGATGC
CCTTACAGGTGAAAAAAATCCAAAATTGAGATGGAAATCCAGAACAAGATGCAACAGCAATCATAGAAGAAAGCAGAACT
TCTTGATAATGAAAAGCCAGATGCTGTGATTGCTCCCGTTACAATGGGATATACAGTGAAAACCAGTAATTATGGATGGG
ATCAGTCAGATAAGTCTGTGAAAATCTACATTACCTTAACTGGAGTTCATCAAGTTCCCACTGAGAATGTGCAGGTGCAT
TTCACAGAGAGGTCATTTGATCTTCTGGTAAAGAATCTAAGTGGGAGGAGTTACTCCATGACTGTGAACAATCTCCTGAA
ACCCATTTCTGTGGAAGGCAGTTCAGAAAAGGTCAAGACTGATACAGTTCTTATTTTATGCAGAAAGAAAGTGGAA

Alignment

ORF - retro_pabe_520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.88 %
• Parental protein coverage: 69.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASEELQKDLEEVKVLLEKATRKRVRDALTAEKS-KIETEIKNK-MQQKSQKKAELLDNEKPAAVVAPITT
          A.EELQK.LEE.KVLL.KATRK.VRDALT.EK..K.........MQQ.S.KKAELLDNEKP.AV.AP.T.
Retrocopy ALEELQKHLEEAKVLLVKATRKGVRDALTGEKNPKLRWKSRTR<MQQQS*KKAELLDNEKPDAVIAPVTM

Parental  GYTVKISNYGWDQSDKFVKIYITLTGVHQVPTENVQVHFTERSFDLLVKNLNGKSYSMIVNNLLKPISVE
          GYTVK.SNYGWDQSDK.VKIYITLTGVHQVPTENVQVHFTERSFDLLVKNL.G.SYSM.VNNLLKPISVE
Retrocopy GYTVKTSNYGWDQSDKSVKIYITLTGVHQVPTENVQVHFTERSFDLLVKNLSGRSYSMTVNNLLKPISVE

Parental  GSSKKVKTDTVLILCRKKVE
          GSS.KVKTDTVLILCRKKVE
Retrocopy GSSEKVKTDTVLILCRKKVE

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	52.36 RPM
SRP007412_cerebellum	0.00 RPM	78.92 RPM
SRP007412_heart	0.03 RPM	21.73 RPM
SRP007412_kidney	0.03 RPM	30.36 RPM
SRP007412_liver	0.00 RPM	13.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_520 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_520 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_706
Pan troglodytes	retro_ptro_505
Gorilla gorilla	retro_ggor_601
Callithrix jacchus	retro_cjac_975

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000170	4 retrocopies	retro_amel_1094, retro_amel_1760, retro_amel_571, retro_amel_975,
Bos taurus	ENSBTAG00000001107	1 retrocopy	retro_btau_1122,
Canis familiaris	ENSCAFG00000029016	1 retrocopy	retro_cfam_1724,
Callithrix jacchus	ENSCJAG00000008989	4 retrocopies	retro_cjac_2432, retro_cjac_3336, retro_cjac_964, retro_cjac_975,
Cavia porcellus	ENSCPOG00000012682	7 retrocopies	retro_cpor_1057, retro_cpor_1207, retro_cpor_1208, retro_cpor_1276, retro_cpor_1462, retro_cpor_581, retro_cpor_759,
Dasypus novemcinctus	ENSDNOG00000015629	1 retrocopy	retro_dnov_915,
Dipodomys ordii	ENSDORG00000001870	1 retrocopy	retro_dord_490,
Erinaceus europaeus	ENSEEUG00000014973	2 retrocopies	retro_eeur_431, retro_eeur_507,
Echinops telfairi	ENSETEG00000009331	3 retrocopies	retro_etel_192, retro_etel_1921, retro_etel_766,
Felis catus	ENSFCAG00000008591	3 retrocopies	retro_fcat_539, retro_fcat_875, retro_fcat_954,
Homo sapiens	ENSG00000116161	2 retrocopies	retro_hsap_2355, retro_hsap_706,
Gorilla gorilla	ENSGGOG00000005962	2 retrocopies	retro_ggor_1788, retro_ggor_601,
Macropus eugenii	ENSMEUG00000010725	5 retrocopies	retro_meug_1472, retro_meug_1517, retro_meug_1751, retro_meug_236, retro_meug_95,
Macaca mulatta	ENSMMUG00000001571	1 retrocopy	retro_mmul_175,
Mustela putorius furo	ENSMPUG00000004813	3 retrocopies	retro_mputfur_1058, retro_mputfur_1122, retro_mputfur_859,
Mus musculus	ENSMUSG00000014226	4 retrocopies	retro_mmus_1443, retro_mmus_2019, retro_mmus_2051, retro_mmus_567,
Nomascus leucogenys	ENSNLEG00000015357	3 retrocopies	retro_nleu_126, retro_nleu_2513, retro_nleu_318,
Oryctolagus cuniculus	ENSOCUG00000004358	3 retrocopies	retro_ocun_1249, retro_ocun_1362, retro_ocun_1852,
Otolemur garnettii	ENSOGAG00000005375	2 retrocopies	retro_ogar_2507, retro_ogar_2720,
Ochotona princeps	ENSOPRG00000000316	1 retrocopy	retro_opri_674,
Procavia capensis	ENSPCAG00000003742	3 retrocopies	retro_pcap_237, retro_pcap_300, retro_pcap_449,
Pongo abelii	ENSPPYG00000000486	3 retrocopies	retro_pabe_207, retro_pabe_2130, retro_pabe_520 ,
Pan troglodytes	ENSPTRG00000001705	2 retrocopies	retro_ptro_1723, retro_ptro_505,
Rattus norvegicus	ENSRNOG00000002572	2 retrocopies	retro_rnor_2734, retro_rnor_589,
Sorex araneus	ENSSARG00000010481	3 retrocopies	retro_sara_646, retro_sara_675, retro_sara_737,
Ictidomys tridecemlineatus	ENSSTOG00000010859	4 retrocopies	retro_itri_1539, retro_itri_732, retro_itri_807, retro_itri_808,
Tursiops truncatus	ENSTTRG00000010399	1 retrocopy	retro_ttru_682,