RetrogeneDB ID: retro_btau_1469

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:99006946..99007177(+)
• Located in intron of: ENSBTAG00000014805

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A2
• Ensembl ID: ENSBTAG00000005096
• Aliases: None
• Description: Cytochrome c oxidase subunit 7A2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P13184]

Sequence

>retro_btau_1469
GCTCTCCGTCAGATTGCTAAGAGGACCATAAGTACTTCTTCACGCAGGCAGTTTGAAAATAAGGTTCCAGAGAAACAAAA
GCTGTTTCAGGAGGATAATGGAATTCCAGTGCATCTGAAGGGTGGGATAGCTGATGCCCTCCTGTATAGAGCCACCATGA
TTCTTACAGTTGGTGGAACGGCATATGCCATGTATGAACTGGCTGTGGCTTCATTTCCCAAGAAGCAGGAT

Alignment

ORF - retro_btau_1469 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 92.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALRQIAKRTISTSSRRQFENKVPEKQKLFQEDNGIPVHLKGGIADALLYRATMILTVGGTAYAMYELAVA
          ALRQIAKRTISTSSRRQFENKVPEKQKLFQEDNGIPVHLKGGIADALLYRATMILTVGGTAYAMYELAVA
Retrocopy ALRQIAKRTISTSSRRQFENKVPEKQKLFQEDNGIPVHLKGGIADALLYRATMILTVGGTAYAMYELAVA

Parental  SFPKKQD
          SFPKKQD
Retrocopy SFPKKQD

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	0.07 RPM	5.34 RPM
ERP005899_muscle	0.37 RPM	76.33 RPM
SRP017611_brain	0.23 RPM	24.94 RPM
SRP017611_kidney	0.30 RPM	59.51 RPM
SRP017611_liver	0.00 RPM	14.20 RPM
SRP030211_testis	1.13 RPM	107.49 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1469 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1469 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1469 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014453	1 retrocopy	retro_amel_723,
Bos taurus	ENSBTAG00000005096	6 retrocopies	retro_btau_1071, retro_btau_1230, retro_btau_1436, retro_btau_1469 , retro_btau_1703, retro_btau_507,
Callithrix jacchus	ENSCJAG00000010305	2 retrocopies	retro_cjac_1523, retro_cjac_4129,
Cavia porcellus	ENSCPOG00000007404	2 retrocopies	retro_cpor_1300, retro_cpor_527,
Dipodomys ordii	ENSDORG00000015425	2 retrocopies	retro_dord_701, retro_dord_790,
Homo sapiens	ENSG00000112695	2 retrocopies	retro_hsap_1434, retro_hsap_2961,
Gorilla gorilla	ENSGGOG00000005865	2 retrocopies	retro_ggor_1104, retro_ggor_2051,
Loxodonta africana	ENSLAFG00000002313	1 retrocopy	retro_lafr_811,
Microcebus murinus	ENSMICG00000015747	3 retrocopies	retro_mmur_381, retro_mmur_548, retro_mmur_799,
Nomascus leucogenys	ENSNLEG00000004949	2 retrocopies	retro_nleu_1412, retro_nleu_735,
Pongo abelii	ENSPPYG00000016781	2 retrocopies	retro_pabe_1187, retro_pabe_2456,
Pteropus vampyrus	ENSPVAG00000010401	6 retrocopies	retro_pvam_1144, retro_pvam_1408, retro_pvam_443, retro_pvam_57, retro_pvam_656, retro_pvam_741,
Rattus norvegicus	ENSRNOG00000042903	1 retrocopy	retro_rnor_52,
Sus scrofa	ENSSSCG00000004480	1 retrocopy	retro_sscr_296,
Ictidomys tridecemlineatus	ENSSTOG00000002536	5 retrocopies	retro_itri_435, retro_itri_464, retro_itri_608, retro_itri_890, retro_itri_892,
Tupaia belangeri	ENSTBEG00000007294	7 retrocopies	retro_tbel_1177, retro_tbel_178, retro_tbel_3617, retro_tbel_4102, retro_tbel_4330, retro_tbel_738, retro_tbel_781,
Tursiops truncatus	ENSTTRG00000007874	1 retrocopy	retro_ttru_669,