RetrogeneDB ID: retro_ecab_697

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 29:29327535..29327981(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000020565
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MCTS1
• Ensembl ID: ENSECAG00000014597
• Aliases: None
• Description: malignant T cell amplified sequence 1 [Source:HGNC Symbol;Acc:23357]

Sequence

>retro_ecab_697
TTCCCAGGCGTGGAGCCCTGGCTGCATCAGATCATGCCCAAGAAGGACCCGGTCAAGATCGTGCGGTGCCACGAGCACAT
AGAGATCCTGACCGTCAACGGGGAGCTGCTGTTCTTCAGACAGAGAGAGGGGCCTTTCTATCCGACTCTGAGGCTGCTCC
ACAAGTACCCCTTCATCCTGCGCGCCAGCAGGTGGATAAGGGCGCCATCAAGTTCGTGCTCAGCGGCGCCAACATCATGT
GTCCCGGCCTGACCTCCCCCGGGGCTCAGCTCTACCCCGCTGCGGAAGACACGGTGGTCGCGATCATGGCGGAGGGCAAG
CAGCACGCCCTGTGTGTGGGCGTCATGAAGATGTCTGCAGAAGACATCGGGAAGGTCAACAAAGGCATCGGCATTGAAAA
CATCCACTATTTAAATGATGGGCTGTGGCATATGAAGACGTATAAA

Alignment

ORF - retro_ecab_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FPVIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLFFRQREGPFYPTLRLLHKYPFIL-PHQQVDKGA
          FP..EPWL.QIMPKKDPVKIVRCHEHIEILTVNGELLFFRQREGPFYPTLRLLHKYPFIL...QQVDKGA
Retrocopy FPGVEPWLHQIMPKKDPVKIVRCHEHIEILTVNGELLFFRQREGPFYPTLRLLHKYPFIL<ARQQVDKGA

Parental  IKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAIMAEGKQHALCVGVMKMSAEDIEKVNKGIGIENIHYLN
          IKFVLSGANIMCPGLTSPGA.LYPAA.DT.VAIMAEGKQHALCVGVMKMSAEDI.KVNKGIGIENIHYLN
Retrocopy IKFVLSGANIMCPGLTSPGAQLYPAAEDTVVAIMAEGKQHALCVGVMKMSAEDIGKVNKGIGIENIHYLN

Parental  DGLWHMKTYK
          DGLWHMKTYK
Retrocopy DGLWHMKTYK

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	5.02 RPM	1.83 RPM
SRP021940_cerebellum	29.08 RPM	1.71 RPM
SRP021940_embryo	23.91 RPM	2.48 RPM
SRP021940_placental_villous	12.12 RPM	2.84 RPM
SRP021940_synovial_membrane	10.46 RPM	3.02 RPM
SRP021940_testis	80.57 RPM	0.83 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_697 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_697 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Equus caballus	ENSECAG00000014597	1 retrocopy	retro_ecab_697 ,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Tupaia belangeri	ENSTBEG00000010666	2 retrocopies	retro_tbel_1485, retro_tbel_4265,