RetrogeneDB ID: retro_btau_1668

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:18473882..18475241(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000034662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UQCRC2
• Ensembl ID: ENSBTAG00000021651
• Aliases: None
• Description: Cytochrome b-c1 complex subunit 2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P23004]

Sequence

>retro_btau_1668
ATGAAACTGTTAACCAGAGCCGGGTCCCTCTCGAGATTTTATTCCCTCAAAGTTGCTCCTAAAGTTAAAGCCACAGCAGC
CCCTGCAGGAGTGCCTCCACATCCTCAGGACCTTGAGTTTACCAGGTTACCAAATGGTTTGGTGATTGCTTCTCTCGAAA
ACTATGCTCCTGCGTCAAGAATTGGTTTGTTCATTAAAGCAGGCAGCAGATATGAGAACTCCAACAATTTAGGAACTTCT
CATTTGCTTCGTCTTGCATCCAGTTTGACTACAAAAGGAGCTTCATCTTTCAAGATAACCCGTGGAATTGAAGCAGTTGG
TGGTAAATTAAGCATGATGTCAACAAGGGAAAACATGGCCTATACTGTGGAATGCCTGCGGGATGATGTTGATATTCTAA
TGGAGTTCCTGCTCAATGTCACCACAGCACCAGAATTTCGACGCTGGGAGGTAGCTGCCCTTCAGCCTCAGCTAAGGATT
GACAAAGCTGTGGCTCTTCAGAATCCACAGGCTTACGTCATTGAAAATTTGCATGCTGCCGCTTACAGAAATGCCTTGGC
TAATTCCTTATATTGTCCTGATTACAGGATTGGAAAAGTGACACCAGTTGAGTTACATGACTATGTACAGAATCATTTTA
CAAGTGCAAGAATGGCTTTGATTGGACTTGGTGTGAGTCATCCTGTCCTAAAGCAAGTTGCTGAACAGTTTCTGAACATA
AGGGGTGGCCTTGGTTTATCTGGTGCAAAAGCCAAGTACCATGGAGGTGAAATTCGGGAACAGAATGGAGACAGTCTCGT
CCATGCCGCTCTTGTAGCAGAGAGTGCAGCCATAGGAAGTGCAGAAGCAAACGTGTTCAGTGTTCTCCAGCACGTCCTCG
GTGCTGGACCACACGTTAAGAGGGGCAGCAATGCCACCAGCTCTCTGTACCAGGCTGTAGCCAAGGGAGTTCACCAACCA
TTTGATGTTTCTGCTTTTAATGCCAGTTACTCAGACTCTGGACTCTTTGGGTTCTACACTATCTCACAAGCTGCATCTGC
TGGAGACGTTATAAAGGCTGCTTATAACCAAGTAAAAACAATTGCTCAAGGAAACCTTTCTAATCCAGATGTCCAAGCTG
CCAAGAACAAGCTGAAAGCTGGGTACCTGATGTCAGTGGAGTCTTCTGAGGGTTTCCTGGATGAAGTTGGGTCCCAGGCT
CTAGCTGCTGGTTCATACACACCGCCATCCACAGTCCTTCAGCAGATTGATGCAGTAGCTGATGCTGATGTCATAAATGC
TGCAAAGAAGTTTGTTTCTGGCCGGAAGTCAATGGCAGCAAGTGGAAATTTGGGGCATACACCTTTCATTGATGAGTTG

Alignment

ORF - retro_btau_1668 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLLTRAGSLSRFYSLKVAPKVKATEAPAGVPPHPQDLEFTRLPNGLVIASLENYAPASRIGLFIKAGSR
          MKLLTRAGSLSRFYSLKVAPKVKAT.APAGVPPHPQDLEFTRLPNGLVIASLENYAPASRIGLFIKAGSR
Retrocopy MKLLTRAGSLSRFYSLKVAPKVKATAAPAGVPPHPQDLEFTRLPNGLVIASLENYAPASRIGLFIKAGSR

Parental  YENSNNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLSVTSTRENMAYTVECLRDDVDILMEFLLNV
          YENSNNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLS..STRENMAYTVECLRDDVDILMEFLLNV
Retrocopy YENSNNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLSMMSTRENMAYTVECLRDDVDILMEFLLNV

Parental  TTAPEFRRWEVAALQPQLRIDKAVALQNPQAHVIENLHAAAYRNALANSLYCPDYRIGKVTPVELHDYVQ
          TTAPEFRRWEVAALQPQLRIDKAVALQNPQA.VIENLHAAAYRNALANSLYCPDYRIGKVTPVELHDYVQ
Retrocopy TTAPEFRRWEVAALQPQLRIDKAVALQNPQAYVIENLHAAAYRNALANSLYCPDYRIGKVTPVELHDYVQ

Parental  NHFTSARMALIGLGVSHPVLKQVAEQFLNIRGGLGLSGAKAKYHGGEIREQNGDSLVHAALVAESAAIGS
          NHFTSARMALIGLGVSHPVLKQVAEQFLNIRGGLGLSGAKAKYHGGEIREQNGDSLVHAALVAESAAIGS
Retrocopy NHFTSARMALIGLGVSHPVLKQVAEQFLNIRGGLGLSGAKAKYHGGEIREQNGDSLVHAALVAESAAIGS

Parental  AEANAFSVLQHVLGAGPHVKRGSNATSSLYQAVAKGVHQPFDVSAFNASYSDSGLFGFYTISQAASAGDV
          AEAN.FSVLQHVLGAGPHVKRGSNATSSLYQAVAKGVHQPFDVSAFNASYSDSGLFGFYTISQAASAGDV
Retrocopy AEANVFSVLQHVLGAGPHVKRGSNATSSLYQAVAKGVHQPFDVSAFNASYSDSGLFGFYTISQAASAGDV

Parental  IKAAYNQVKTIAQGNLSNPDVQAAKNKLKAGYLMSVESSEGFLDEVGSQALAAGSYTPPSTVLQQIDAVA
          IKAAYNQVKTIAQGNLSNPDVQAAKNKLKAGYLMSVESSEGFLDEVGSQALAAGSYTPPSTVLQQIDAVA
Retrocopy IKAAYNQVKTIAQGNLSNPDVQAAKNKLKAGYLMSVESSEGFLDEVGSQALAAGSYTPPSTVLQQIDAVA

Parental  DADVINAAKKFVSGRKSMAASGNLGHTPFIDEL
          DADVINAAKKFVSGRKSMAASGNLGHTPFIDEL
Retrocopy DADVINAAKKFVSGRKSMAASGNLGHTPFIDEL

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	1.44 RPM	54.94 RPM
ERP005899_muscle	1.16 RPM	135.09 RPM
SRP017611_brain	0.55 RPM	58.56 RPM
SRP017611_kidney	7.53 RPM	127.08 RPM
SRP017611_liver	0.15 RPM	49.61 RPM
SRP030211_testis	4.15 RPM	98.78 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1668 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1668 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021651	2 retrocopies	retro_btau_1008, retro_btau_1668 ,
Canis familiaris	ENSCAFG00000017756	1 retrocopy	retro_cfam_2075,
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Homo sapiens	ENSG00000140740	1 retrocopy	retro_hsap_2785,
Gorilla gorilla	ENSGGOG00000015379	1 retrocopy	retro_ggor_1941,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Macaca mulatta	ENSMMUG00000018287	2 retrocopies	retro_mmul_1442, retro_mmul_683,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Nomascus leucogenys	ENSNLEG00000012185	1 retrocopy	retro_nleu_685,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Pongo abelii	ENSPPYG00000007174	1 retrocopy	retro_pabe_2232,
Pan troglodytes	ENSPTRG00000007871	1 retrocopy	retro_ptro_1886,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Tupaia belangeri	ENSTBEG00000010785	1 retrocopy	retro_tbel_3988,