RetrogeneDB ID: retro_btau_1064

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 25:32708..33335(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG1
• Ensembl ID: ENSBTAG00000006607
• Aliases: None
• Description: Cyclin-G1 [Source:UniProtKB/Swiss-Prot;Acc:Q5E9I1]

Sequence

>retro_btau_1064
ATCAAGGTACAGCCCAAGCACCTTGGGTGTGTTGGACTAAGCTGCTTCTATCTGGCTGTAAAATCAACAGAAGAGGAAAG
GAATGTCCCATTGGCAACTGACTTGATCCGAATAAGCCAGTACAGGTTCACGGTTTCAGACTTGATGAGAATGGAGAAGA
TCGTATTGGAGAAGGTGTGTTGGAAAGTCAAAGCTACTACTGCCTTTCAGTTTCTACAGCTCTATTACTCACTCCTTCAA
GAGAACGTGCCACATGAAAGGAAGAGTAGCCTTAATTTTGAAAGGCTAGAAGCCCAACTTAAGGCATGCTACTGCAGGAT
CATATTTTCTAAAGCAAAGCCATCTGTGTTGGCATTGTCTGTCATCGCATTGGAGATCCAAGCACAGAAGTATATAGAGT
TAACAGAAGGAGTAGAACGTCTTCAGAAACATTCCAAGATCAGTGGCAGAGATTTGACTTTCTGGCAGGAGCTTGTATCC
AAGTGTTTAGCTGAATATTCATCGAACAAGTGTGCCAAACCAAACGTTCAGAAGTTGAAATGGATTGTTTCTGGGCGTAC
TGCACGGCAACTGAGGCATAGTTACTACAGGATAACCCACCTTCCAACAATTCCCGAAACGGTCCCT

Alignment

ORF - retro_btau_1064 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.04 %
• Parental protein coverage: 70.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKVQPKHLGCVGLSCFYLAVKSTEEERNVPLATDLIRISQYRFTVSDLMRMEKIVLEKVCWKVKATTAFQ
          .KVQPKHLGCVGLSCFYLAVKSTEEERNVPLATDLIRISQYRFTVSDLMRMEKIVLEKVCWKVKATTAFQ
Retrocopy IKVQPKHLGCVGLSCFYLAVKSTEEERNVPLATDLIRISQYRFTVSDLMRMEKIVLEKVCWKVKATTAFQ

Parental  FLQLYYSLLQENVPHERKSSLNFERLEAQLKACYCRIIFSKAKPSVLALSIIALEIQAQKYIELTEGVER
          FLQLYYSLLQENVPHERKSSLNFERLEAQLKACYCRIIFSKAKPSVLALS.IALEIQAQKYIELTEGVER
Retrocopy FLQLYYSLLQENVPHERKSSLNFERLEAQLKACYCRIIFSKAKPSVLALSVIALEIQAQKYIELTEGVER

Parental  LQKHSKISGRDLTFWQELVSKCLAEYSSNKCAKPNVQKLKWIVSGRTARQLRHSYYRITHLPTIPETVP
          LQKHSKISGRDLTFWQELVSKCLAEYSSNKCAKPNVQKLKWIVSGRTARQLRHSYYRITHLPTIPETVP
Retrocopy LQKHSKISGRDLTFWQELVSKCLAEYSSNKCAKPNVQKLKWIVSGRTARQLRHSYYRITHLPTIPETVP

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	70.94 RPM
ERP005899_muscle	1.16 RPM	747.44 RPM
SRP017611_brain	0.27 RPM	44.26 RPM
SRP017611_kidney	0.47 RPM	122.46 RPM
SRP017611_liver	0.00 RPM	44.55 RPM
SRP030211_testis	0.16 RPM	30.32 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1064 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1064 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006607	2 retrocopies	retro_btau_1064 , retro_btau_763,
Canis familiaris	ENSCAFG00000017207	1 retrocopy	retro_cfam_1657,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Dipodomys ordii	ENSDORG00000014293	1 retrocopy	retro_dord_486,
Equus caballus	ENSECAG00000018880	1 retrocopy	retro_ecab_152,
Felis catus	ENSFCAG00000027366	1 retrocopy	retro_fcat_763,
Myotis lucifugus	ENSMLUG00000001667	1 retrocopy	retro_mluc_1341,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Otolemur garnettii	ENSOGAG00000007639	1 retrocopy	retro_ogar_2452,
Pteropus vampyrus	ENSPVAG00000017902	1 retrocopy	retro_pvam_1027,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351,