RetrogeneDB ID: retro_ecab_467

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:1156176..1156740(-)
• Located in intron of: ENSECAG00000010484

Retrocopy information

• Ensembl ID: ENSECAG00000013867
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRELID1
• Ensembl ID: ENSECAG00000023460
• Aliases: None
• Description: PRELI domain containing 1 [Source:HGNC Symbol;Acc:30255]

Sequence

>retro_ecab_467
AGCAAACATGTCTCGATGGAGACAGTACACCGGGAGGTGACCCCTGACCAGAAGCTCCTGTCCCGGCGACTCCTGACCAA
GACCAACAGGATGCCCCGCTGGGCCGAGCGACTGTTTCCTGCCAATGTTGCTCACTCAGTGTACATCCTGGAGGATTCTA
TTGTGGACCCACAGAACCAGATCATGACCACCTTCATCTGGAACGTCAACCATGCCCAGCTGATGGTGGTGGAGGAACGA
TGTGTTTACTGTCTGAACTCTGATAACAGTGGCTGGACCGAAATCCTCCAGGAAGCCTGGGTCTCCTCTAGCTTATTTGG
CATCTCCAGAGCTGTCCAGGAATTTGGTCTGGCCCGGTTCAAAAGCAACGTGACCAAGACTATGAAGGGTTTTGAGTACA
TCTTGGCCAAGCTGCAAGGCGAGGCTCCTTCCAAATCCCTTGTGGAGACAGCCAAGGAAGCCAAGGAGAAGGCAAGGGAG
ACGGCACTGGCAGCTACGGAGAAGGCCAAGGACCTTGCCAGCAAGGCCGCCACCAAGAAGCAGCAGCAGCAGCAGCAGTT
CGTG

Alignment

ORF - retro_ecab_467 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.42 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERLFPANVAHSVYILEDSIVDPQNQTMTTFTWNI
          SKHV..E..VHREVTPDQKLLSRRLLTKTNRMPRWAERLFPANVAHSVYILEDSIVDPQNQ.MTTF.WN.
Retrocopy SKHVSMET-VHREVTPDQKLLSRRLLTKTNRMPRWAERLFPANVAHSVYILEDSIVDPQNQIMTTFIWNV

Parental  NHARLMVVEERCVYCVNSDNSGWTEIRREAWVSSSLFGVSRAVQEFGLARFKSNVTKTMKGFEYILAKLQ
          NHA.LMVVEERCVYC.NSDNSGWTEI..EAWVSSSLFG.SRAVQEFGLARFKSNVTKTMKGFEYILAKLQ
Retrocopy NHAQLMVVEERCVYCLNSDNSGWTEILQEAWVSSSLFGISRAVQEFGLARFKSNVTKTMKGFEYILAKLQ

Parental  GEAPSKSLVETAKEAKEKARETALAATEKAKDLASKAANKKQQQQQQFV
          GEAPSKSLVETAKEAKEKARETALAATEKAKDLASKAA.K.......FV
Retrocopy GEAPSKSLVETAKEAKEKARETALAATEKAKDLASKAATKXXXXXXXFV

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	1.48 RPM	48.76 RPM
SRP021940_cerebellum	4.21 RPM	67.36 RPM
SRP021940_embryo	3.12 RPM	75.23 RPM
SRP021940_placental_villous	4.76 RPM	78.90 RPM
SRP021940_synovial_membrane	2.66 RPM	71.21 RPM
SRP021940_testis	2.11 RPM	50.52 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_467 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_467 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_467 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002251	1 retrocopy	retro_chof_1025,
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Cavia porcellus	ENSCPOG00000025788	1 retrocopy	retro_cpor_231,
Dasypus novemcinctus	ENSDNOG00000017550	1 retrocopy	retro_dnov_637,
Equus caballus	ENSECAG00000023460	1 retrocopy	retro_ecab_467 ,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Macaca mulatta	ENSMMUG00000009046	2 retrocopies	retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mus musculus	ENSMUSG00000021486	7 retrocopies	retro_mmus_1316, retro_mmus_2079, retro_mmus_2236, retro_mmus_2394, retro_mmus_2672, retro_mmus_449, retro_mmus_866,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Rattus norvegicus	ENSRNOG00000016410	8 retrocopies	retro_rnor_1138, retro_rnor_1166, retro_rnor_1243, retro_rnor_1906, retro_rnor_2178, retro_rnor_2305, retro_rnor_637, retro_rnor_995,