RetrogeneDB ID: retro_ecab_78

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:817668..818988(+)
• Located in intron of: ENSECAG00000013539

Retrocopy information

• Ensembl ID: ENSECAG00000006237
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000015200
• Aliases: None
• Description: None

Sequence

>retro_ecab_78
ATGGCTTTAGATCTCAGAATCTCATTTCAAGGTGAACCATCCAGGAATGATCCTGGGTTAGAAAATCACGAGTTTAATCC
CAGTCAAGTACCTGCTGTCCAAGAGGGGGAGGGGATCTCTGAGTTCCCGAGCACTCAACACAGCTTATTTCAAATTGGCA
AGAACTCATGTACAAGGAAGGAACTGCAAAGACTCTATAAGTTATTTCACTCCTGGCTACAGCCAGAAAAACAAAGCAAG
GATGAAATGATTTCTTGTTTGGTCCTGGAACAATTTATGATCAATGGCTACTGCAGTGACAGGTCCATGTTGAAAGAGAA
ATGGGAATCAAGTGGCAGAAACCTGGAGAAATTCATGGAAGATCTGACCGATGATGGCATGAAGCCACCTTGCTTAGTCC
ACGTCTGCATGCAGGGGCAGGACGCTCTCTTTTCTGAGAACATGCCCTTAAGAGAAGTCATCGTTCACCTCACAAAACAG
TTGTTAACAGGAACCCCAACTGGAGAGAACATGGGGACCCCTTTCGGGACTCCCAAAGATCATTCCCTGGAAACAGAACA
AGGAGATGAAGATAAAGAAAATGGTGGCAACATTTCTTTGAAAACTTGTCAAGTAAATGACAGTATGACTAGTCAAGACA
ATCAAACGCCTTCCCTACTCATCATCCAGGGAGAGAACCGGCCTGGGCCTGGAGAGGGAGGTGTTCCTTTGGAGAATCCA
CTCAGCTCCAGAAGAGCAGGTCTAGGCACCTGCAGGTCCCAGGAAGAGTCCCTGAAAGGACCCCCTTATCAAGATGTCGT
TATAGAGGTGGGACCAGGGTTTCTCTCCCGGGCAAACCAGGTTATGCCTGAGTGTGTTCCTACCCACCAGAGCATTGAGG
GAAACTCAGCATGTGGGGGACACCAAGAAAGATCCCACAGAGCCCCCAAATCATACAAATGTGAGAAGTGTCCCAGGATC
TTTAGGTATCTGTCTCGGTTAAAAGCCCATCAAAGAAGACACAATAATGAGAGGACATTTATTTGTGGCCAGTGTGACAA
AGGCTTCTTCCAGGCATCAGACCTACGCGTGCAACAGAAGATTCACACAGGAGAGAAACCTTTCAAATGCAGCACATGTG
AAATGTCCTTCAGCCACAAAACCAACCTTCGGGCTCATGAGAGAATCCACACAGGGGAGAAGCCCTATGTGTGTTCCCTT
TGCCAGAGAAGCTACCACCAGTCATCCACCTACCACCGCCACCTGAGGACTCACCAGAAAATTGCTTTCAAAAGTGTTCC
CTCCACACCAGATGCTTCCTCGGGTACAGTGCCAATGTAA

Alignment

ORF - retro_ecab_78 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALDLRISFQGEPSRNDPGSENHEFNPRQVPAVQDGERISKFPSTQHSLFQNGKNSCARQELQRLYKLFH
          MALDLRISFQGEPSRNDPG.ENHEFNP.QVPAVQ.GE.IS.FPSTQHSLFQ.GKNSC.R.ELQRLYKLFH
Retrocopy MALDLRISFQGEPSRNDPGLENHEFNPSQVPAVQEGEGISEFPSTQHSLFQIGKNSCTRKELQRLYKLFH

Parental  SWLQPEKHSKDEMISRLVLEQFMINGYCSDRSMLKEKWESSGRNLEKFMEDLTDDGMKPPGLVHVCMQGQ
          SWLQPEK.SKDEMIS.LVLEQFMINGYCSDRSMLKEKWESSGRNLEKFMEDLTDDGMKPP.LVHVCMQGQ
Retrocopy SWLQPEKQSKDEMISCLVLEQFMINGYCSDRSMLKEKWESSGRNLEKFMEDLTDDGMKPPCLVHVCMQGQ

Parental  EALFSENMPLREVIVHLRKQFSTGTQTGENMGTPFQTPKDHSLETEQGDEDKENGGNISLKTCQVNDSMT
          .ALFSENMPLREVIVHL.KQ..TGT.TGENMGTPF.TPKDHSLETEQGDEDKENGGNISLKTCQVNDSMT
Retrocopy DALFSENMPLREVIVHLTKQLLTGTPTGENMGTPFGTPKDHSLETEQGDEDKENGGNISLKTCQVNDSMT

Parental  SQGNQTPSLLIIQGENRPGPGEGGVPLENPLSSRRAGLGSCRSQEESLKGPPYQDVLIEVRPGFLSRPNQ
          SQ.NQTPSLLIIQGENRPGPGEGGVPLENPLSSRRAGLG.CRSQEESLKGPPYQDV.IEV.PGFLSR.NQ
Retrocopy SQDNQTPSLLIIQGENRPGPGEGGVPLENPLSSRRAGLGTCRSQEESLKGPPYQDVVIEVGPGFLSRANQ

Parental  VTPERVPTHQSIEGNSACGGHQERSQGAPKSYKCEKCPRIFRYLSRLKAHQRRHNNERTFICGQCDKGFF
          V.PE.VPTHQSIEGNSACGGHQERS..APKSYKCEKCPRIFRYLSRLKAHQRRHNNERTFICGQCDKGFF
Retrocopy VMPECVPTHQSIEGNSACGGHQERSHRAPKSYKCEKCPRIFRYLSRLKAHQRRHNNERTFICGQCDKGFF

Parental  QASDLRMHQKIHTGEKPFKCSTCEMSFSHKTNLRAHERIHTGEKPYVCSLCQRSYRQSSTYHRHLRTHQK
          QASDLR..QKIHTGEKPFKCSTCEMSFSHKTNLRAHERIHTGEKPYVCSLCQRSY.QSSTYHRHLRTHQK
Retrocopy QASDLRVQQKIHTGEKPFKCSTCEMSFSHKTNLRAHERIHTGEKPYVCSLCQRSYHQSSTYHRHLRTHQK

Parental  IAFKSVPS
          IAFKSVPS
Retrocopy IAFKSVPS

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.03 RPM	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	0.06 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_78 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_78 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_78 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005419	2 retrocopies	retro_cpor_1470, retro_cpor_285,
Dasypus novemcinctus	ENSDNOG00000011483	11 retrocopies	retro_dnov_1048, retro_dnov_1253, retro_dnov_1287, retro_dnov_1505, retro_dnov_174, retro_dnov_1780, retro_dnov_2499, retro_dnov_2556, retro_dnov_2666, retro_dnov_859, retro_dnov_964,
Equus caballus	ENSECAG00000015200	1 retrocopy	retro_ecab_78 ,
Loxodonta africana	ENSLAFG00000003257	1 retrocopy	retro_lafr_171,
Ictidomys tridecemlineatus	ENSSTOG00000023779	1 retrocopy	retro_itri_408,