RetrogeneDB ID: retro_ecab_198

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:168625802..168626155(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS10
• Ensembl ID: ENSECAG00000006430
• Aliases: None
• Description: ribosomal protein S10 [Source:HGNC Symbol;Acc:10383]

Sequence

>retro_ecab_198
ATGTTGATGCCCATGAAGAACTGGATTGCCATTTATGAACTTCTTTTGAAGGAGACAGTCATGTTGCCAAGAAGGACGTC
AACATGCCAAAGCACCCCAAGCTGGCAGGAAAGAATGTGCCCAATCTTCATGTCACCAAGGCCACGCGGTCTCTCAAGTC
ACAATGCTACTGAAGAAACGGTTTGCTGGAGGCATTTCTACTGGTGCCTCACCAACAAGGGTTGCCAGTATCTCCGTGAT
TACCACCATCTGCCCCCTGGGGTCGTGTGTGCCACCCTGCACCACAGCCATCCTGAGACTGGCAGGCCAGGCCGAAAGGG
CTGGAGGGCGAGTGGCCCGCAGGACTCACCAGA

Alignment

ORF - retro_ecab_198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.36 %
• Parental protein coverage: 71.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLMPKKNR-AIYELPFKEGVM-VAK-DVHMPKHPELADKNVPNLHVMKAMQSLKSRGY-VKEQFA-WRHF
          MLMP.KN..AIYEL..KE.VM.VAK.DV.MPKHP.LA.KNVPNLHV.KA..SLKS..Y..K..FA.WRHF
Retrocopy MLMPMKNWIAIYELLLKETVM<VAKKDVNMPKHPKLAGKNVPNLHVTKATRSLKSQCY<LKKRFA<WRHF

Parental  YWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRP-RPKGLEGERPARLTR
          YW.LTN.G.QYLRDY.HLPP..V.ATL..S.PETGRP.RPKGLEGE.PA.LTR
Retrocopy YWCLTNKGCQYLRDYHHLPPGVVCATLHHSHPETGRP<RPKGLEGEWPAGLTR

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	540.12 RPM
SRP021940_cerebellum	0.00 RPM	353.14 RPM
SRP021940_embryo	0.61 RPM	596.97 RPM
SRP021940_placental_villous	0.43 RPM	328.45 RPM
SRP021940_synovial_membrane	0.77 RPM	454.17 RPM
SRP021940_testis	0.32 RPM	365.50 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_198 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_198 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015250	4 retrocopies	retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Equus caballus	ENSECAG00000006430	1 retrocopy	retro_ecab_198 ,
Homo sapiens	ENSG00000124614	24 retrocopies	retro_hsap_1509, retro_hsap_1628, retro_hsap_1630, retro_hsap_1657, retro_hsap_1923, retro_hsap_2003, retro_hsap_2113, retro_hsap_229, retro_hsap_2415, retro_hsap_2573, retro_hsap_2574, retro_hsap_2830, retro_hsap_289, retro_hsap_3007, retro_hsap_3170, retro_hsap_3243, retro_hsap_3436, retro_hsap_3454, retro_hsap_3720, retro_hsap_4114, retro_hsap_4190, retro_hsap_460, retro_hsap_869, retro_hsap_992,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Macaca mulatta	ENSMMUG00000000267	2 retrocopies	retro_mmul_332, retro_mmul_555,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Mus musculus	ENSMUSG00000052146	9 retrocopies	retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Oryctolagus cuniculus	ENSOCUG00000011373	2 retrocopies	retro_ocun_250, retro_ocun_874,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Rattus norvegicus	ENSRNOG00000000490	4 retrocopies	retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,
Ictidomys tridecemlineatus	ENSSTOG00000013486	5 retrocopies	retro_itri_1448, retro_itri_1515, retro_itri_230, retro_itri_787, retro_itri_963,