RetrogeneDB ID: retro_ecab_55

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:26120170..26121430(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004415
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000017166
• Aliases: None
• Description: None

Sequence

>retro_ecab_55
ATGAACGTTCACTGTGGCAGTGAGAGTGACAGGTTCCTGCGGCCAGAGGCCAGCTGCCTGATGGATGAAACCTCAGCTGC
AGCCCAAGAAAAAGAAACAAATAATCTGACTTCTTCTGGTCTTCAAACCCTTGCTTATCCTCTAGGTCCCAGGAATGATG
ACCTTTCACTCGACCCTGCATCTCAGCCAGCAAATCTTCAGTTCCCGCACGTAATGCCACTTCCCGAAGACATCAAAGGC
TCTTGCTTACAGAGTGGGAATAAGCGTAACCATGACCCCTTTCTTGCTCCAGAACGATTTGGAAACAGCACTGTGGGCTT
TGGCAGTAATGTTCATTCCCAGGCACCAGAGAAAGTGACTCTTCTCGTAGATGGCACACGTTTTGTTGTGAATCCACAAA
TTTTCACTGCTCATCCAGATACCATGTTGGGAAGGATGTTTGGACCAGGAAGAGAGTACAACTTCACGCGGCCCAACGAG
AAGGGGGAGTATGAGATTGCTGAAGGAATCAGTGCAGCTGTGTTTCAAACGGTGCTGGATTATTACAAAACTGGTATCAT
CAATTGTCCTGATGGCATCTCTATCCCAGACCTTAGAGACACGTGCGATTATCTCTGCATTAACTTTGACTTCAACACTA
TCCGATGTCAGGATCTGAGTGCTTTACTGCATGAACTGTCTAACGACGGTGCTCACAAGCAGTTTGATCACTACCTCGAA
GAGCTGATCCTGCCCATCATGGTGGGCTGTGCCAAGAAGGGTGAGCGCGAGTGCCATATCGTTGTGCTGACAGATGAGGA
TTCTGTGGACTGGGATGAAGACCACCCCCCACCCATGGGGGAGGAATATTCCCAAATTCTTTACAGCTCTAAGCTCTACA
GATTCTTCAAGTACATTGAGAATCGGGATGTCGCCAAAACAGTGTTAAAGGAGCGGGGCCTGAAAAACATTCGCATTGGA
ATTGAAGGTTACCCTACCTGTAAAGAAAAAATTAAGAGAAGACCTGGTGGCCGATCTGAAGTAATCTATAATTATGTGCA
GCGCCCCTTTATCCAGATGTCGTGGGAAAAGGAAGAAGGAAAGAGTCGCCATGTGGATTTCCAGTGTGTTCGAAGCAAAT
CCCTCACTAATCTGGTAGCTGCTGGAGAAGACGTCTTAGAGGACCAGGAGATACTAATGTACCACCCACCCCAAGTGGAT
GAACTTGACCGGCTAAATGCCCCACTTTCTCAGATGGCCTCTAATGACTTTCAGGATTAG

Alignment

ORF - retro_ecab_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNVHCGSESDRFLRPEASCLMDETSAAAQEKETNNLTSSGLQTLAYPLGPRNDDLSLDPASQPANLQFPH
          MNVHCGSESDRFLRPEASCLMDETSAAAQEKETNNLTSSGLQTLAYPLGPRNDDLSLDPASQPANLQFPH
Retrocopy MNVHCGSESDRFLRPEASCLMDETSAAAQEKETNNLTSSGLQTLAYPLGPRNDDLSLDPASQPANLQFPH

Parental  VMPLPEDIKGSCFQSGNKRNHDPFLAPERFGNSTVGFGSNVHSQAPEKVTLLVDGTRFVVNPQIFTAHPD
          VMPLPEDIKGSC.QSGNKRNHDPFLAPERFGNSTVGFGSNVHSQAPEKVTLLVDGTRFVVNPQIFTAHPD
Retrocopy VMPLPEDIKGSCLQSGNKRNHDPFLAPERFGNSTVGFGSNVHSQAPEKVTLLVDGTRFVVNPQIFTAHPD

Parental  TMLGRMFGPGREYNFTRPNEKGEYEIAEGISAAVFRTVLDYYKTGIINCPDGISIPDLRDTCDYLCINFD
          TMLGRMFGPGREYNFTRPNEKGEYEIAEGISAAVF.TVLDYYKTGIINCPDGISIPDLRDTCDYLCINFD
Retrocopy TMLGRMFGPGREYNFTRPNEKGEYEIAEGISAAVFQTVLDYYKTGIINCPDGISIPDLRDTCDYLCINFD

Parental  FNTIRCQDLSALLHELSNDGAHKQFDHYLEELILPIMVGCAKKGERECHIVVLTDEDSVDWDEDHPPPMG
          FNTIRCQDLSALLHELSNDGAHKQFDHYLEELILPIMVGCAKKGERECHIVVLTDEDSVDWDEDHPPPMG
Retrocopy FNTIRCQDLSALLHELSNDGAHKQFDHYLEELILPIMVGCAKKGERECHIVVLTDEDSVDWDEDHPPPMG

Parental  EEYSQILYSSKLYRFFKYIENRDVAKTVLKERGLKNIRIGIEGYPTCKEKIKRRPGGRSEVIYNYVQRPF
          EEYSQILYSSKLYRFFKYIENRDVAKTVLKERGLKNIRIGIEGYPTCKEKIKRRPGGRSEVIYNYVQRPF
Retrocopy EEYSQILYSSKLYRFFKYIENRDVAKTVLKERGLKNIRIGIEGYPTCKEKIKRRPGGRSEVIYNYVQRPF

Parental  IQMSWEKEEGKSRHVDFQCVRSKSLTNLVAAGEDVLEDQEVLMYHPPQVDELDRLNAPLSQMASNDFQD
          IQMSWEKEEGKSRHVDFQCVRSKSLTNLVAAGEDVLEDQE.LMYHPPQVDELDRLNAPLSQMASNDFQD
Retrocopy IQMSWEKEEGKSRHVDFQCVRSKSLTNLVAAGEDVLEDQEILMYHPPQVDELDRLNAPLSQMASNDFQD

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	1.89 RPM
SRP021940_cerebellum	0.05 RPM	7.01 RPM
SRP021940_embryo	0.15 RPM	13.50 RPM
SRP021940_placental_villous	0.05 RPM	6.40 RPM
SRP021940_synovial_membrane	0.27 RPM	9.11 RPM
SRP021940_testis	0.06 RPM	4.22 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_55 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_55 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_55 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017166	1 retrocopy	retro_ecab_55 ,
Myotis lucifugus	ENSMLUG00000007139	1 retrocopy	retro_mluc_1744,
Tarsius syrichta	ENSTSYG00000012406	1 retrocopy	retro_tsyr_2108,