RetrogeneDB ID: retro_btau_835

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:112675346..112675853(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000027962
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDHC
• Ensembl ID: ENSBTAG00000015853
• Aliases: None
• Description: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P35720]

Sequence

>retro_btau_835
ATGGCTGCGCTCTTGTTGAGACATGTTGGCCGTCACTGCCTCCGTGCCCACCTTAGTCCTCAGCTCTGTATCAGAAATGC
TGTTCCTTTGGGAACCACAGCCAAAGAAGAGATGGAGAGGTTCTGGAGTAAGAACACTAGTTTAAACCGTCCTTTGTCTC
CCCATATCAGCATCTACGGCTGGTCTCTTCCCATGGCGATGTCCATTTGCCACCGTGGCACTGGTATTGCCTTGAGTGCA
GGAGTCTCTCTTTTTGGCTTGTCAGCCCTCTTGGTCCCTGGGAGCTTTGAGTCTCATTTGGAATTTGTGAAGTCCCTGTG
TTTGGGGCCAGCACTGATCCACACAGCCAAATTTGCACTTGTCTTCCCTCTCATGTATCACACCTGGAATGGGATCCGAC
ACTTGATGTGGGATCTAGGAAAAGGCCTGACGATTTCCCAGCTACACCAGTCTGGAGAGGCTGTCCTGGTTCTTACTGTG
TTGTCCTCTGTAGGGCTGGCAGCCATG

Alignment

ORF - retro_btau_835 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALLLRHVGRHCLRAHLSPQLCIRNAVPLGTTAKEEMERFWSKNTTLNRPLSPHISIYGWSLPMAMSIC
          MAALLLRHVGRHCLRAHLSPQLCIRNAVPLGTTAKEEMERFWSKNT.LNRPLSPHISIYGWSLPMAMSIC
Retrocopy MAALLLRHVGRHCLRAHLSPQLCIRNAVPLGTTAKEEMERFWSKNTSLNRPLSPHISIYGWSLPMAMSIC

Parental  HRGTGIALSAGVSLFGLSALLVPGSFESHLEFVKSLCLGPALIHTAKFALVFPLMYHTWNGIRHLMWDLG
          HRGTGIALSAGVSLFGLSALLVPGSFESHLEFVKSLCLGPALIHTAKFALVFPLMYHTWNGIRHLMWDLG
Retrocopy HRGTGIALSAGVSLFGLSALLVPGSFESHLEFVKSLCLGPALIHTAKFALVFPLMYHTWNGIRHLMWDLG

Parental  KGLTISQLHQSGVAVLVLTVLSSVGLAAM
          KGLTISQLHQSG.AVLVLTVLSSVGLAAM
Retrocopy KGLTISQLHQSGEAVLVLTVLSSVGLAAM

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	5.41 RPM	73.54 RPM
ERP005899_muscle	5.91 RPM	79.34 RPM
SRP017611_brain	2.19 RPM	13.52 RPM
SRP017611_kidney	13.87 RPM	70.06 RPM
SRP017611_liver	8.83 RPM	53.08 RPM
SRP030211_testis	2.38 RPM	16.95 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_835 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
GH328925	112675421	112675635	99.6	213	1	212

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_835 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_835 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015351	2 retrocopies	retro_amel_468, retro_amel_803,
Bos taurus	ENSBTAG00000015853	1 retrocopy	retro_btau_835 ,
Canis familiaris	ENSCAFG00000012992	2 retrocopies	retro_cfam_1529, retro_cfam_275,
Callithrix jacchus	ENSCJAG00000004757	3 retrocopies	retro_cjac_1119, retro_cjac_2455, retro_cjac_988,
Echinops telfairi	ENSETEG00000015767	1 retrocopy	retro_etel_675,
Felis catus	ENSFCAG00000000499	1 retrocopy	retro_fcat_1609,
Homo sapiens	ENSG00000143252	4 retrocopies	retro_hsap_1794, retro_hsap_1896, retro_hsap_609, retro_hsap_854,
Gorilla gorilla	ENSGGOG00000008017	3 retrocopies	retro_ggor_1390, retro_ggor_536, retro_ggor_697,
Macaca mulatta	ENSMMUG00000012411	11 retrocopies	retro_mmul_1063, retro_mmul_1323, retro_mmul_1338, retro_mmul_1686, retro_mmul_1845, retro_mmul_2002, retro_mmul_2087, retro_mmul_239, retro_mmul_2416, retro_mmul_369, retro_mmul_672,
Mustela putorius furo	ENSMPUG00000014439	1 retrocopy	retro_mputfur_1201,
Nomascus leucogenys	ENSNLEG00000014367	3 retrocopies	retro_nleu_1476, retro_nleu_420, retro_nleu_439,
Pan troglodytes	ENSPTRG00000001585	4 retrocopies	retro_ptro_1274, retro_ptro_2458, retro_ptro_449, retro_ptro_593,
Pteropus vampyrus	ENSPVAG00000005544	2 retrocopies	retro_pvam_879, retro_pvam_974,
Rattus norvegicus	ENSRNOG00000003163	2 retrocopies	retro_rnor_1486, retro_rnor_1487,
Sarcophilus harrisii	ENSSHAG00000016835	1 retrocopy	retro_shar_205,
Sus scrofa	ENSSSCG00000030318	2 retrocopies	retro_sscr_1050, retro_sscr_1061,
Takifugu rubripes	ENSTRUG00000001873	1 retrocopy	retro_trub_41,
Tursiops truncatus	ENSTTRG00000009234	1 retrocopy	retro_ttru_196,