RetrogeneDB ID: retro_ecab_226

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:4078645..4079438(-)
• Located in intron of: ENSECAG00000009914

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADCK4
• Ensembl ID: ENSECAG00000022458
• Aliases: None
• Description: aarF domain containing kinase 4 [Source:HGNC Symbol;Acc:19041]

Sequence

>retro_ecab_226
ATGTGGCTGGAGGTAGGGGGCCTCCTGCGGGGGACCTGTGGACAGCTGGGTCGGACTGGTGGTCTGCCTTGTGGGGCCCC
GAGGCCTGGGCCCCACTGGTGGGGGCCATGTGGGGGTTCTTGGGCCCAAAAGCTTCATCAGGATGGGCCCGGCAGAGGTG
TGGGTGAGGAAGACATCCGCCGGGCACGGGAGGCCCAGATCAGGAAGACACCCCGGCCCCAGCTGAGTGACCGCTCTGGA
GAACGCAAGGTGCCCGCCTCCCGCATCAGCCGCTTGGCCAACTTTGGGGGACTGGGCTGTGGGCTTGGGACTGGGAGCGC
TGGCTGAGGTGGCTAAGAAGTCCCTGCCAGGAGGACATCGACAATCAGAAGGCAGCTCCCGGCCAGGCTCCAGCCCGTTG
CTGTCGGAGGCCAACGCCGAGCGGGTTGTGCAGACCTTGTGTACAGTTCGAGGGGCCGCCCTCAAGGTTGGCCAAATGCT
CAGCATCCAGGACAACAGCTTCATCAGCCCCCAGCTGCAGCGCATCTCCGAGCGGGTCTGCCAGAGCGCCGACTTCATGC
CCCGCTGGCAGATGCTGAGAGTTCTCGAGGAGGAGCTCGGCACAGACTGGCAGGCCAAGGTGGCCTTTTTGGAGGAGGTG
CCCTTTGCTGCTGTCTCAATTGGGCAGGTGCACCAGGGCCTGCTGAGGGACGGGACAGAGGTTGCCATGAAGATCCAGTA
CCCAGGCGTTGCCCAGAGCATTCAGAGCAATGTGCAGAACCTGCTGGCGGTGCTCAAGATGGGCGTGGCCCTG

Alignment

ORF - retro_ecab_226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.72 %
• Parental protein coverage: 50.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MWLEVGGLLRGTCGQLGRTVGLPCGAPRPGPHWWGPCGGSWAQKLHQDGPGRGLGEEDIRRAREARIRKT
          MWLEVGGLLRGTCGQLGRT.GLPCGAPRPGPHWWGPCGGSWAQKLHQDGPGRG.GEEDIRRAREA.IRKT
Retrocopy MWLEVGGLLRGTCGQLGRTGGLPCGAPRPGPHWWGPCGGSWAQKLHQDGPGRGVGEEDIRRAREAQIRKT

Parental  PRPQLSDRSRERKVPASRISRLANFGGL-AVGLGLGALAEVAKKSLPGGHRQSEGSSRPGSSPLLTEANA
          PRPQLSDRS.ERKVPASRISRLANFGGL.AVGLGLGALAEVAKKSLPGGHRQSEGSSRPGSSPLL.EANA
Retrocopy PRPQLSDRSGERKVPASRISRLANFGGL>AVGLGLGALAEVAKKSLPGGHRQSEGSSRPGSSPLLSEANA

Parental  ERVVQTLCTVRGAALKIGQMLSIQDNSFISPQLQRIFERVRQSADFMPRWQMLRVLEEELGTDWQAKVAS
          ERVVQTLCTVRGAALK.GQMLSIQDNSFISPQLQRI.ERV.QSADFMPRWQMLRVLEEELGTDWQAKVA.
Retrocopy ERVVQTLCTVRGAALKVGQMLSIQDNSFISPQLQRISERVCQSADFMPRWQMLRVLEEELGTDWQAKVAF

Parental  LEEVPFAAASIGQVHQGLLRDGTEVAVKIQYPGVAQSIQSDVQNLLAVLKMSVAL
          LEEVPFAA.SIGQVHQGLLRDGTEVA.KIQYPGVAQSIQS.VQNLLAVLKM.VAL
Retrocopy LEEVPFAAVSIGQVHQGLLRDGTEVAMKIQYPGVAQSIQSNVQNLLAVLKMGVAL

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	5.61 RPM
SRP021940_cerebellum	0.05 RPM	16.25 RPM
SRP021940_embryo	0.08 RPM	16.57 RPM
SRP021940_placental_villous	0.05 RPM	16.26 RPM
SRP021940_synovial_membrane	0.05 RPM	14.91 RPM
SRP021940_testis	0.19 RPM	16.82 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_226 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_226 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_226 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000022458	1 retrocopy	retro_ecab_226 ,