RetrogeneDB ID: retro_ecab_106

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:183874748..183875276(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000005219
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSECAG00000009563
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_ecab_106
ATGAGGAAGGTGCTGTTCAGTTTCTTTGGGAACAAGGAGCTGCGGATCCTCATGCTGGGCCTGGACGCGGCCGGCAAGAC
CACCATCCTGTACAAGCTGAAGCTCGGCCAGTCGGTGACCACCATCCCCACGGTGGGCTTCAACGTGGAGACGGTGACTT
ACAAAAACGTCAAGTTCAACGTGTGGGACGTGGGCGGCCAGGACAAGATCCGGCCGCTCTGGCGGCACTACTACACCGGG
ACCCAGGGCCTGATCTTCGTGGTGGACTGCGCCGACCGCGACCGCATCGACGAGGCCCGCCAGGAGCTGCACCGCATCAT
CAACGACCGGGAGATGCGGGACGCCATCATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCATGAAGCCCCACG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCGTGTGCCACCTCGGGGGAC
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCCTAA

Alignment

ORF - retro_ecab_106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.36 %
• Parental protein coverage: 95.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLFKSLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRP
          K...S.FG.KE.RILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIRP
Retrocopy KVLFSFFGNKELRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRP

Parental  LWRHYFQNTQGLIFVVDSNDRERVNEAREELTRMLAEDELRDAVLLVFVNKQDLPNAMNAAEITDKLGLH
          LWRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.F.NKQDLP.AM...EI..KLGL.
Retrocopy LWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLT

Parental  SLRQRNWYIQATCATSGDGLYEGLDWLSNQLKN
          ..R.RNWY.Q..CATSGDGLYEGL.WL....K.
Retrocopy RIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

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	41.44 RPM	5.90 RPM
SRP021940_cerebellum	19.53 RPM	19.21 RPM
SRP021940_embryo	34.50 RPM	12.45 RPM
SRP021940_placental_villous	61.20 RPM	12.27 RPM
SRP021940_synovial_membrane	67.34 RPM	12.93 RPM
SRP021940_testis	29.86 RPM	7.16 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_106 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_106 has 12 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_36
Pan troglodytes	retro_ptro_5
Gorilla gorilla	retro_ggor_161
Pongo abelii	retro_pabe_126
Macaca mulatta	retro_mmul_174
Callithrix jacchus	retro_cjac_300
Mus musculus	retro_mmus_147
Rattus norvegicus	retro_rnor_272
Oryctolagus cuniculus	retro_ocun_132
Bos taurus	retro_btau_26
Sus scrofa	retro_sscr_82
Canis familiaris	retro_cfam_119

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004184	1 retrocopy	retro_amel_1639,
Bos taurus	ENSBTAG00000006785	1 retrocopy	retro_btau_26,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Equus caballus	ENSECAG00000009563	1 retrocopy	retro_ecab_106 ,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Mus musculus	ENSMUSG00000062421	1 retrocopy	retro_mmus_2056,
Oryctolagus cuniculus	ENSOCUG00000023198	1 retrocopy	retro_ocun_132,
Otolemur garnettii	ENSOGAG00000002503	1 retrocopy	retro_ogar_263,
Ictidomys tridecemlineatus	ENSSTOG00000019768	1 retrocopy	retro_itri_883,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,