RetrogeneDB ID: retro_cfam_1657

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:42203861..42204744(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG1
• Ensembl ID: ENSCAFG00000017207
• Aliases: None
• Description: cyclin G1 [Source:HGNC Symbol;Acc:1592]

Sequence

>retro_cfam_1657
ATGATAGAAGTACTGACAACTGAATCTCAGAAATTGCTACACCAGCTGAATGCCCTATTGGAACAGGAGTCCAGATGTCA
GCCAAAGGTCTGCAGCTTGAGACTAATTGAATCTGCACACGATAATGGCCTCAGAATGACTGCAAGACTAAGGGACTTTG
AAGTAAAAGATCTTCTTAGTCTAACTCAGTTCTTTGGCTTTGACACGGAGACATTTTCTCTAGCTGTGAATTTACTGGAC
AGATTCCTGTCCAAAATGAAGGTACAGCCCAAGCACCTTGGCTGTGTTGGGCTGAGCTGCTTCTATTTGGCTGTTAAATC
AATAGAAGAGGAAAGGAATGTCCCATTGGCAACTGACTTGATCCGAATAAGCCAGTATAGGTTCACGGTTTCAAACTTGA
TGAGAATGGAAAAGATTATATTGGAGAAAGTGTGTTGAAAAGTCAAAGCTACTACTGCCTTTCAATTTCTGCAACTCTAC
AAACTCACTCATTCAAGAGAACTTACCAATTGAAAGGAAGAATAGCCTTAATTTTGAAAGACTAGAAGTTCAACTTAAGG
CATGCCACTGCAGGATCATATTTTCTAAAGCAAAGCCTTCTGTGTTGGCATTGTCTATCATTGCACTGGAGATCGAAGCA
CAGAAGTTTGTAGAGTTAACTGAAGGAATAGAATGTCTTCAGATACATTCCAAGATAAATGGCAGAGATTTGACCTTCTG
GCAAGAACTTGTATCCAAGTGTTTAACTGAATATTCATCAAACAAGTGTTCCAAAGCCAATGTTCAGAAGTTGAAATGGA
TTGTTTCTGGACGTACTGCACGGTAATTGAAGCATAGTTACTACAGAATAACCCACCTTCCAACAACTCCTGAAATGGTC
CCT

Alignment

ORF - retro_cfam_1657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIEVLTTTESQKLLHQLNALLEQESRCQPKVCGLRLIESAHDNGLRMTARLRDFEVKDLLSLTQFFGFDT
          MIEVLTT.ESQKLLHQLNALLEQESRCQPKVC.LRLIESAHDNGLRMTARLRDFEVKDLLSLTQFFGFDT
Retrocopy MIEVLTT-ESQKLLHQLNALLEQESRCQPKVCSLRLIESAHDNGLRMTARLRDFEVKDLLSLTQFFGFDT

Parental  ETFSLAVNLLDRFLSKMKVQPKHLGCVGLSCFYLAVKSIEEERNVPLATDLIRISQYRFTVSDLMRMEKI
          ETFSLAVNLLDRFLSKMKVQPKHLGCVGLSCFYLAVKSIEEERNVPLATDLIRISQYRFTVS.LMRMEKI
Retrocopy ETFSLAVNLLDRFLSKMKVQPKHLGCVGLSCFYLAVKSIEEERNVPLATDLIRISQYRFTVSNLMRMEKI

Parental  VLEKVCWKVKATTAFQFLQLY-YSLIQENLPIERKNSLNFERLEAQLKACHCRIIFSKAKPSVLALSIIA
          .LEKVC.KVKATTAFQFLQLY..SLIQENLPIERKNSLNFERLE.QLKACHCRIIFSKAKPSVLALSIIA
Retrocopy ILEKVC*KVKATTAFQFLQLY>NSLIQENLPIERKNSLNFERLEVQLKACHCRIIFSKAKPSVLALSIIA

Parental  LEIQAQKFVELTEGIECLQTHSKINGRDLTFWQELVSKCLTEYSSNKCSKPNVQKLKWIVSGRTARQLKH
          LEI.AQKFVELTEGIECLQ.HSKINGRDLTFWQELVSKCLTEYSSNKCSK.NVQKLKWIVSGRTAR.LKH
Retrocopy LEIEAQKFVELTEGIECLQIHSKINGRDLTFWQELVSKCLTEYSSNKCSKANVQKLKWIVSGRTAR*LKH

Parental  SYYRITHLPTIPEMVP
          SYYRITHLPT.PEMVP
Retrocopy SYYRITHLPTTPEMVP

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
SRP012049_cerebellum	0.08 RPM	40.53 RPM
SRP017611_brain	0.16 RPM	30.96 RPM
SRP017611_kidney	3.10 RPM	265.27 RPM
SRP017611_liver	0.00 RPM	17.04 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1657 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1657 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,