RetrogeneDB ID: retro_ecab_1038

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: Un0019:744318..745283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASB1
• Ensembl ID: ENSECAG00000014057
• Aliases: None
• Description: ankyrin repeat and SOCS box containing 1 [Source:HGNC Symbol;Acc:16011]

Sequence

>retro_ecab_1038
AGTGCAGGTCCTAATCTGAAGGAGTGGCTGAGGGAGCAGTTTTGTGACCATCCGCTAGAGCACTGCGAGGACACCAGGCT
CCATGATGCAGCCTGCGTGGGGGACCTCCAGACCCTCAGGAGCCTGTTACAAGAGGAGGGCTACCGGAGCCGCATCAACG
AGAAATCTGTCTGGTGCTGTGGCTGGCTGCCCTGCACACCACTGCGAATCGCGGCCACTGCTGGCCGTGGGAACTGTGTG
GACTTCCTGATCCAGAAGGGGGCCGAGGTGGATCTGGTGGATGTAAAGGGACAAGACTGCCCTGTATGTGGCTGTGGTGA
ACGGGCACCTGGAGAGTGCCCAGATCCTCCTTGAAGCCGGCGCCGACCCCAACGGAAGCCGGCACCATCGCAGTACGCCT
GTCTACCACGCCTCTCGTGTGGGCAGGGCCGACATACTGAAGGCTCTCATCAGGTATGGGGCTGATGTCGATGTCAACCA
CCACCTGACTCCAGACATCCGGCCCCCTTTTTCCCCGGCGCCTCAGCTCCTTGGTCGTCTGCCCCTTGTACATCAGCGCG
GCCTACCACAACCTCCAGTGCTTCAAGCTGCTCCTCCAGGCTAGGGCGAACCCCGACTTCAACTGCAACGGCCCTGTCAA
CACGCAGGGCTTCTACAGGGGCTCCCCCGGGTGCGTCATGGATGCAGTCCTGCGTCATGGCTGTGAGGCGGCCTTTGTGA
GCCTGCTCGTAGCGTGTGGAGCGAACCTGAACCTGGTGAAGTGGGAATCCTTGGGCCCAGAGTCGAGAGGCAGAAGGAAG
GCCGACCCCGAGGCATTGCACGTCTTTAAAGAGGCCAGAAGTGTCCCCAGGACCTTGCTGAATCTGTGCAGTCTGGCCGT
GAGAAGAGCTCTTGGCAAATACTGACTCCATCTGATTTCTTCGCTGCCTCTGCCAGACCCCATAAAGAAGTTTCTACTTT
ATGAG

Alignment

ORF - retro_ecab_1038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAGPNLKEWLREQFCDHPLEHCEDTRLHDAAYVGDLQTLRSLLQEEGYRSRINEKSVWCCGWLPCTPLRI
          SAGPNLKEWLREQFCDHPLEHCEDTRLHDAA.VGDLQTLRSLLQEEGYRSRINEKSVWCCGWLPCTPLRI
Retrocopy SAGPNLKEWLREQFCDHPLEHCEDTRLHDAACVGDLQTLRSLLQEEGYRSRINEKSVWCCGWLPCTPLRI

Parental  AATAGHGNCVDFLIQKGAEVDLVDVKGQ-TALYVAVVNGHLESAQILLEAGADPNGSRHHRSTPVYHASR
          AATAG.GNCVDFLIQKGAEVDLVDVKGQ.TALYVAVVNGHLESAQILLEAGADPNGSRHHRSTPVYHASR
Retrocopy AATAGRGNCVDFLIQKGAEVDLVDVKGQ>TALYVAVVNGHLESAQILLEAGADPNGSRHHRSTPVYHASR

Parental  VGRADILKALIRYGADVDVNHHLTPDIRPPFS-RRLTSLVVCPLYISAAYHNLQCFKLLLQAGANPDFNC
          VGRADILKALIRYGADVDVNHHLTPDIRPPFS.RRL.SLVVCPLYISAAYHNLQCFKLLLQA.ANPDFNC
Retrocopy VGRADILKALIRYGADVDVNHHLTPDIRPPFS>RRLSSLVVCPLYISAAYHNLQCFKLLLQARANPDFNC

Parental  NGPVNTQGFYRGSPGCVMDAVLRHGCEAAFVSLLVEFGANLNLVKWESLGPESRGRRKVDPEALQVFKEA
          NGPVNTQGFYRGSPGCVMDAVLRHGCEAAFVSLLV..GANLNLVKWESLGPESRGRRK.DPEAL.VFKEA
Retrocopy NGPVNTQGFYRGSPGCVMDAVLRHGCEAAFVSLLVACGANLNLVKWESLGPESRGRRKADPEALHVFKEA

Parental  RSVPRTLLNLCRVAVRRALGKYRLHLIPSLPLPDPIKKFLLYE
          RSVPRTLLNLC..AVRRALGKY.LHLI.SLPLPDPIKKFLLYE
Retrocopy RSVPRTLLNLCSLAVRRALGKY*LHLISSLPLPDPIKKFLLYE

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	0.30 RPM	5.84 RPM
SRP021940_cerebellum	0.52 RPM	25.29 RPM
SRP021940_embryo	0.82 RPM	14.42 RPM
SRP021940_placental_villous	0.05 RPM	3.42 RPM
SRP021940_synovial_membrane	0.11 RPM	7.47 RPM
SRP021940_testis	0.32 RPM	31.65 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1038 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1038 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	ENSECAG00000014057	1 retrocopy	retro_ecab_1038 ,