RetrogeneDB ID: retro_btau_474

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:58979630..58980606(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000021503
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSBTAG00000020908
• Aliases: None
• Description: Nucleosome assembly protein 1-like 1 [Source:UniProtKB/Swiss-Prot;Acc:A6H767]

Sequence

>retro_btau_474
ATCGACAACTTGCCTAGGGTAGTTAAAAGACGAGTGAATGCTCTCAAAAACCTTCAAGTTAAATGTGCACAGATAGAAGC
CAAATTCTATGAGGAAGTTCATGATCTTGAAAGAAAGTATGCTGTTCTTTATCAGCCTCTGTTTGATAAGCAATTTGAGA
TCATTAATGCCATTTATGAACCTACAGAAGAAGAGTGTGAATGGAAACCAGATGAGGAAGATGAAATTTCGGAGGAGCTA
AAAGAAAAGGCCAAGATTGAAGATGAGAAAAAGGATGAAGAAAAAGAAGATCCCAAGGGAATTCCTGAGTTTTGGTTGAT
CGTTTTTAAGAATGTTGACTTGCTCAGTGATATGGTTCAGGAACATGATGAGCCTATTCTGAAGCACTTGAAAGATATTG
AAGTGAAGTTCTCAGATGCTGGTCAGCCTATGAGTTTTGTCTTAGAATTGCACTTTGAACCCAATGAATATTTCACAAAT
GAAGTGTTGACAAAGACATATAGGATGAGGTCAGAACCAGATGATTCTGATCCCTTTTCTTTTGATGGACCAGTAATTAT
GGGTTGTACAGGGTGCCAGATAGATTGGAAAAAAGGCAAGAATGTCACTTTGAAAACGATTAAGAAGAAGCAGAAACACA
AGGGACGTGGGACAGTTTGTACTGTGACCAAAACAGTTTCTAATGACTCTTTCTTTAATTTTTTTTGCCCCTCCTGAAGT
TCCTGAGAGTGGAGATCTGGATGATGATTCTGAAGCTATCCTCGCTGCAGACTTTGAAATTGGTCACTTTTTACGTGAGC
GTATAATCCCAAGATCAGTGTTATACTTTACTGGAGAAGCTATTGAAGACGACGATGATGACTATGATGAAGAAGGTGAA
GAAGCGGATGAGGAAGGGGAAGAAGAAGGAGATGAGGAAAATGATCCAGATTATGACCCAAAGAAGGATCAAAACCCAGC
AGAGTGCAAGCAGCAG

Alignment

ORF - retro_btau_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.28 %
• Parental protein coverage: 83.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IESLPRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAIYEPTEEECEWKP
          I..LPRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDK.FEIINAIYEPTEEECEWKP
Retrocopy IDNLPRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKQFEIINAIYEPTEEECEWKP

Parental  DEEDEISEELKEKAKVEDEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDA
          DEEDEISEEL.................PKGIPEFWL.VFKNVDLLSDMVQEHDEPILKHLKDI.VKFSDA
Retrocopy DEEDEISEELXXXXXXXXXXXXXXXXXPKGIPEFWLIVFKNVDLLSDMVQEHDEPILKHLKDIEVKFSDA

Parental  GQPMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKK
          GQPMSFVLE.HFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGP.IMGCTGCQIDWKKGKNVTLKTIKKK
Retrocopy GQPMSFVLELHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPVIMGCTGCQIDWKKGKNVTLKTIKKK

Parental  QKHKGRGTVRTVTKTVSNDSFF-NFFAPPEVPESGDLDDDSEAILAADFEIGHFLRERIIPRSVLYFTGE
          QKHKGRGTV.TVTKTVSNDSFF....APPEVPESGDLDDDSEAILAADFEIGHFLRERIIPRSVLYFTGE
Retrocopy QKHKGRGTVCTVTKTVSNDSFF>XXXAPPEVPESGDLDDDSEAILAADFEIGHFLRERIIPRSVLYFTGE

Parental  AIEDDDDDYDEEGEEADEEGEEEGDEENDPDYDPKKDQNPAECKQQ
          AIEDDDDD...................NDPDYDPKKDQNPAECKQQ
Retrocopy AIEDDDDDXXXXXXXXXXXXXXXXXXXNDPDYDPKKDQNPAECKQQ

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
ERP005899_liver	0.00 RPM	23.14 RPM
ERP005899_muscle	0.63 RPM	187.24 RPM
SRP017611_brain	1.51 RPM	93.19 RPM
SRP017611_kidney	0.53 RPM	64.37 RPM
SRP017611_liver	0.23 RPM	26.05 RPM
SRP030211_testis	0.44 RPM	113.21 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_474 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_474 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474 , retro_btau_652, retro_btau_70, retro_btau_935,
Choloepus hoffmanni	ENSCHOG00000003210	2 retrocopies	retro_chof_1095, retro_chof_2057,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Felis catus	ENSFCAG00000000279	1 retrocopy	retro_fcat_1037,
Homo sapiens	ENSG00000187109	3 retrocopies	retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Nomascus leucogenys	ENSNLEG00000004682	4 retrocopies	retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Oryctolagus cuniculus	ENSOCUG00000013857	1 retrocopy	retro_ocun_834,
Otolemur garnettii	ENSOGAG00000010319	4 retrocopies	retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pongo abelii	ENSPPYG00000004786	2 retrocopies	retro_pabe_2287, retro_pabe_999,
Pan troglodytes	ENSPTRG00000005240	4 retrocopies	retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Pteropus vampyrus	ENSPVAG00000016032	2 retrocopies	retro_pvam_1282, retro_pvam_306,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Ictidomys tridecemlineatus	ENSSTOG00000003046	2 retrocopies	retro_itri_1007, retro_itri_416,
Tursiops truncatus	ENSTTRG00000017062	2 retrocopies	retro_ttru_160, retro_ttru_1921,
Vicugna pacos	ENSVPAG00000007290	3 retrocopies	retro_vpac_435, retro_vpac_441, retro_vpac_601,