RetrogeneDB ID: retro_ecab_152

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:159027667..159028328(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000015257
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNG1
• Ensembl ID: ENSECAG00000018880
• Aliases: None
• Description: cyclin G1 [Source:HGNC Symbol;Acc:1592]

Sequence

>retro_ecab_152
AAACTGCTCCACCAGCTGAATGCCCTGTTGGAACAGGAGTCCGGATGTCAGCCAGAGGTCTGTGGCTTGAGACTAATTGA
ATCTGCACACGATAATGGTCTGAGAATGACTGCAAGGCTCAGGGAATTTGAAGTAAAAGCTCTTAGTCTAACTCAGTTCT
TTGGCTTCAACACAGAGACGTTTTCTCTAGCTGTGAATTTATTGGAGAGTTTCCTTTCCAAAATGGACGTACCACCCAAG
CAGCTTGGGTGTGTTGGGCTGAGCTGCTTCTATTTGGCTGTAAAATCAATAGAAGAGGAAAGGAATGTCCCATCGGCAAC
TGATTTGATCCAAATAAGCCAGTATAGGTTCACGGTTTCAGACTTGGTGAGAAAGGAAAAGATTGTGTTGGAGAAGGTGT
GTTGGAAAGTCAAAGCTGCTACTGCCTTTCAATTTCTGCCAACTCTATTATTCACTCACTCAAGGGAATTTGCCATTTGA
AAGGAAGAATGGCCTTAATTTTGAAAGACTAGAAGTTCAACTTAAGGCATGTTACTGCAGGATCATATTTTCTAAAGCAA
AGCTTTCTGTTTTGGCATTGTCTATGACTCCATTGGAGAGCCAAGCCCAGAAGTGTGTAGATTTAACAGAAGGAGTAGAA
TGTCTTCAGAAGCATTCCAAG

Alignment

ORF - retro_ecab_152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.84 %
• Parental protein coverage: 75.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLLHQLNALLEQESRCQPKVCGLRLIESAHDNGLRMTARLRDFEVKDLLSLTQFFGFDTETFSLAVNLLD
          KLLHQLNALLEQES.CQP.VCGLRLIESAHDNGLRMTARLR.FEVK..LSLTQFFGF.TETFSLAVNLL.
Retrocopy KLLHQLNALLEQESGCQPEVCGLRLIESAHDNGLRMTARLREFEVK-ALSLTQFFGFNTETFSLAVNLLE

Parental  RFLSKMKVQPKHLGCVGLSCFYLAVKSIEEERNVPLATDLIRISQYRFTVSDLMRMEKIVLEKVCWKVKA
          .FLSKM.V.PK.LGCVGLSCFYLAVKSIEEERNVP.ATDLI.ISQYRFTVSDL.R.EKIVLEKVCWKVKA
Retrocopy SFLSKMDVPPKQLGCVGLSCFYLAVKSIEEERNVPSATDLIQISQYRFTVSDLVRKEKIVLEKVCWKVKA

Parental  TTAFQFL-QLYYSLIQENLPFERKNSLNFERLEAQLKACYCRIIFSKAKPSVLALSIIALEIQAQKCVEL
          .TAFQFL.QLYYSL.Q.NLPFERKN.LNFERLE.QLKACYCRIIFSKAK.SVLALS...LE.QAQKCV.L
Retrocopy ATAFQFL>QLYYSLTQGNLPFERKNGLNFERLEVQLKACYCRIIFSKAKLSVLALSMTPLESQAQKCVDL

Parental  TEGVECLQKHSK
          TEGVECLQKHSK
Retrocopy TEGVECLQKHSK

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
SRP021940_articular_cartilage	0.00 RPM	182.87 RPM
SRP021940_cerebellum	0.00 RPM	12.98 RPM
SRP021940_embryo	0.03 RPM	129.19 RPM
SRP021940_placental_villous	0.00 RPM	63.22 RPM
SRP021940_synovial_membrane	0.00 RPM	55.07 RPM
SRP021940_testis	0.00 RPM	16.18 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_152 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_152 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,