RetrogeneDB ID: retro_ecab_1090

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:98672531..98672849(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000015816
• Aliases: None
• Description: None

Sequence

>retro_ecab_1090
ATGTCGAACATCTCCCCCTTCTCCCTTGGGCTATCATCCAGCAGGTGTTTGATCATGGCAGTATCTACAACTCTCAAGTG
CTTGACGTCACGGAGGAAACTTTGCATTCTTGCTTCCTGGGTGTCTGTAATGTTGCCTGCATATGTCTGCAGATTGGTTA
CCCAGCTGTCACGTCAGTACCCCCGTTCTATCACCAGTGGGGACAAGTGGGTCCTCGCTTTGCTTGTGGAGACTGATTAC
ACCTTCCCACTTGCTGAGAAGATCAAGGCCACTGACACCACTGCTGCTCCTGTTGCTGCCGCAGCCCCAGTCAAGGCT

Alignment

ORF - retro_ecab_1090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.64 %
• Parental protein coverage: 75.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLNISPFSFGL-IIQQVFDNGSIYNPEVLDITEETLHSRFLEGVRNVASVCLQIGYPTVASVP-HSIING
          M.NISPFS.GL.IIQQVFD.GSIYN..VLD.TEETLHS.FL.GV.NVA..CLQIGYP.V.SVP..SI..G
Retrocopy MSNISPFSLGL<IIQQVFDHGSIYNSQVLDVTEETLHSCFL-GVCNVACICLQIGYPAVTSVP>RSITSG

Parental  YKRVLALSVETDYTFPLAEKVKAFLADPSAFVAAAPVAA
          .K.VLAL.VETDYTFPLAEK.KA.........AAAPV.A
Retrocopy DKWVLALLVETDYTFPLAEKIKATDTTAAPVAAAAPVKA

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	0.06 RPM	2549.85 RPM
SRP021940_cerebellum	0.00 RPM	505.56 RPM
SRP021940_embryo	0.10 RPM	1287.74 RPM
SRP021940_placental_villous	0.10 RPM	862.44 RPM
SRP021940_synovial_membrane	0.22 RPM	1580.66 RPM
SRP021940_testis	0.32 RPM	753.44 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1090 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1090 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003756	2 retrocopies	retro_acar_111, retro_acar_115,
Choloepus hoffmanni	ENSCHOG00000002745	2 retrocopies	retro_chof_1115, retro_chof_2341,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Equus caballus	ENSECAG00000015816	2 retrocopies	retro_ecab_1090 , retro_ecab_585,
Homo sapiens	ENSG00000089157	7 retrocopies	retro_hsap_1403, retro_hsap_1553, retro_hsap_1889, retro_hsap_2095, retro_hsap_2334, retro_hsap_512, retro_hsap_784,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macropus eugenii	ENSMEUG00000016409	12 retrocopies	retro_meug_1211, retro_meug_1245, retro_meug_1339, retro_meug_1410, retro_meug_1672, retro_meug_1689, retro_meug_1789, retro_meug_1800, retro_meug_1943, retro_meug_2166, retro_meug_294, retro_meug_772,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Procavia capensis	ENSPCAG00000016429	6 retrocopies	retro_pcap_232, retro_pcap_314, retro_pcap_339, retro_pcap_353, retro_pcap_408, retro_pcap_67,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,
Tursiops truncatus	ENSTTRG00000005658	1 retrocopy	retro_ttru_965,