RetrogeneDB ID: retro_ptro_2491

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:148336026..148336936(-)
• Located in intron of: ENSPTRG00000018686

Retrocopy information

• Ensembl ID: ENSPTRG00000042108
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KATNBL1
• Ensembl ID: ENSPTRG00000006877
• Aliases: None
• Description: katanin p80 subunit B-like 1 [Source:HGNC Symbol;Acc:26199]

Sequence

>retro_ptro_2491
ATGGCATCGGAAACTCACAATGTTAAAAAACGGAACTTTTGTAATAAGATTGAGGATCATTTCATTGATCTTCCTAGAAA
AAACGATCTCTAATTTCACTAATAAGAACATGAAGGAGGTTAAGAAGTCTCCAAAACAGTTGGCTGCTTACATAAATAGA
ACAGTTGGACAAACTGTGAAAAGCCCAGATAAACTTCGTAAAGTGATCTATCTCAGAAAGAAAGTTCATCATCCCTTTCC
AAATCTTTGTTACAGAAAAAAACAGCCCCCTGGAAGTGGGGGCTGTGACATGGCAAATAAAGAAAATGAACTGGCTTGTG
CAGGCCACCTGCCTGAAAAATTACACCATGACAGTCGAACATATTTGGTTAACTCCAGTGATTCTGGTTCTTCACAGACA
GAAAGCCCATCATCAAAATATACTGGGTTTTTTTCTGAGGTTTCTCAGGACCATGAAACAATGGTCCAAGTTTTGTTCAG
CAGGAATATGAGATTGAATGTAGCTTTAATTTTCTGGAGAAAGAGAAGTATAAGTGAACTTGTAGCTTATTTGTTGAGGA
TAGAAGATCTTGGCGTTGTGGTAGATTGCCTTCCTGTGCTCACCAATTGTTTACAGGAAGAAAAACAATATATCTCATTT
GGTTGCTGTGTAGACTTATTGCCTCTAGTAAAGTCACTACTTAAAAGCAAATTTGAAGAATATGTTATAGTTGGTTTAAA
CTGGCTTCAAGCAGTCATTAAAAGGTGGTGGTCAGAACTATCATCCGAAACAGAAATTTTAAATGATGGAAATATTCAAA
TTTTAAAACAATTAAGTGGATTATGGGAACAGGAAAACCATCTTACTTTGGTTCCAGGATATACTGGTAATATAGCTAAG
GATGTAGATGCCTATTTATTACAGTTACAT

Alignment

ORF - retro_ptro_2491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASETHNVKKRNFCNKIEDHFIDLPRKK-ISNFTNKNMKEVKKSPKQLAAYINRTVGQTVKSPDKLRKVI
          MASETHNVKKRNFCNKIEDHFIDLPRK..ISNFTNKNMKEVKKSPKQLAAYINRTVGQTVKSPDKLRKVI
Retrocopy MASETHNVKKRNFCNKIEDHFIDLPRKN>ISNFTNKNMKEVKKSPKQLAAYINRTVGQTVKSPDKLRKVI

Parental  YRRKKVHHPFPNPCYRKKQSPGSGGCDMANKENELACAGHLPEKLHHDSRTYLVNSSDSGSSQTESPSSK
          Y.RKKVHHPFPN.CYRKKQ.PGSGGCDMANKENELACAGHLPEKLHHDSRTYLVNSSDSGSSQTESPSSK
Retrocopy YLRKKVHHPFPNLCYRKKQPPGSGGCDMANKENELACAGHLPEKLHHDSRTYLVNSSDSGSSQTESPSSK

Parental  YSGFFSEVSQDHETMAQVLFSRNMRLNVALTFWRKRSISELVAYLLRIEDLGVVVDCLPVLTNCLQEEKQ
          Y.GFFSEVSQDHETM.QVLFSRNMRLNVAL.FWRKRSISELVAYLLRIEDLGVVVDCLPVLTNCLQEEKQ
Retrocopy YTGFFSEVSQDHETMVQVLFSRNMRLNVALIFWRKRSISELVAYLLRIEDLGVVVDCLPVLTNCLQEEKQ

Parental  YISLGCCVDLLPLVKSLLKSKFEEYVIVGLNWLQAVIKRWWSELSSKTEIINDGNIQILKQQLSGLWEQE
          YIS.GCCVDLLPLVKSLLKSKFEEYVIVGLNWLQAVIKRWWSELSS.TEI.NDGNIQILK.QLSGLWEQE
Retrocopy YISFGCCVDLLPLVKSLLKSKFEEYVIVGLNWLQAVIKRWWSELSSETEILNDGNIQILK-QLSGLWEQE

Parental  NHLTLVPGYTGNIAKDVDAYLLQLH
          NHLTLVPGYTGNIAKDVDAYLLQLH
Retrocopy NHLTLVPGYTGNIAKDVDAYLLQLH

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	0.05 RPM	11.69 RPM
SRP007412_cerebellum	0.04 RPM	10.75 RPM
SRP007412_heart	0.00 RPM	4.08 RPM
SRP007412_kidney	0.00 RPM	9.26 RPM
SRP007412_liver	0.00 RPM	4.58 RPM
SRP007412_testis	0.11 RPM	6.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2491 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2491 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3677
Gorilla gorilla	retro_ggor_2486

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006413	2 retrocopies	retro_btau_1198, retro_btau_1776,
Callithrix jacchus	ENSCJAG00000021110	3 retrocopies	retro_cjac_1971, retro_cjac_265, retro_cjac_2971,
Cavia porcellus	ENSCPOG00000011153	2 retrocopies	retro_cpor_1374, retro_cpor_1410,
Dasypus novemcinctus	ENSDNOG00000016279	5 retrocopies	retro_dnov_1586, retro_dnov_2201, retro_dnov_2253, retro_dnov_248, retro_dnov_957,
Dipodomys ordii	ENSDORG00000013172	2 retrocopies	retro_dord_378, retro_dord_730,
Equus caballus	ENSECAG00000023450	1 retrocopy	retro_ecab_841,
Echinops telfairi	ENSETEG00000001640	7 retrocopies	retro_etel_1169, retro_etel_1341, retro_etel_2032, retro_etel_2062, retro_etel_319, retro_etel_518, retro_etel_635,
Homo sapiens	ENSG00000134152	3 retrocopies	retro_hsap_3171, retro_hsap_3677, retro_hsap_425,
Gorilla gorilla	ENSGGOG00000014230	3 retrocopies	retro_ggor_1347, retro_ggor_2486, retro_ggor_415,
Macropus eugenii	ENSMEUG00000015610	4 retrocopies	retro_meug_1035, retro_meug_1899, retro_meug_1900, retro_meug_646,
Myotis lucifugus	ENSMLUG00000001532	2 retrocopies	retro_mluc_214, retro_mluc_633,
Macaca mulatta	ENSMMUG00000000013	1 retrocopy	retro_mmul_2005,
Mustela putorius furo	ENSMPUG00000008019	1 retrocopy	retro_mputfur_1258,
Nomascus leucogenys	ENSNLEG00000010772	2 retrocopies	retro_nleu_1020, retro_nleu_2679,
Oryctolagus cuniculus	ENSOCUG00000017654	5 retrocopies	retro_ocun_1065, retro_ocun_343, retro_ocun_614, retro_ocun_877, retro_ocun_975,
Otolemur garnettii	ENSOGAG00000015633	3 retrocopies	retro_ogar_1643, retro_ogar_2219, retro_ogar_3301,
Ochotona princeps	ENSOPRG00000010379	1 retrocopy	retro_opri_446,
Pongo abelii	ENSPPYG00000006309	2 retrocopies	retro_pabe_2634, retro_pabe_646,
Pan troglodytes	ENSPTRG00000006877	3 retrocopies	retro_ptro_2271, retro_ptro_2491 , retro_ptro_323,
Sorex araneus	ENSSARG00000007891	1 retrocopy	retro_sara_345,
Ictidomys tridecemlineatus	ENSSTOG00000003813	1 retrocopy	retro_itri_1292,