RetrogeneDB ID: retro_ecab_58

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:115716039..115716393(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006641
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSECAG00000019719
• Aliases: None
• Description: ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]

Sequence

>retro_ecab_58
ATGGTCCAGCGTTTGACCTACCGCCATAGGCTCTCCTACAACACAGCGTCTAACAAAACGAGGCTGTCCCGAACCCCTGG
TAATAGGATTGTTTACCTTTATACCAAGAAAGTTGGGAAAGCACCGAAGTCCGCGTGTGGCGTGTGCCCAGGCCGACTGC
AAGGCGTTCGTGCTGTGAGGCCTAAAGTTCTTATGAGATTGTCTAAAACGAAAAAACACGTCAGCAGGGCCTACGGAGGT
TCCATGTGTGCTAAATGTGTCCGCGACAGGATCAAGCATGCTTTCCTTATTGAGGAGCAGAAAATCGTTGTGAAAGTGTT
GAAGGCACAAGCACAGAGTCAGAAAGCTAAATAA

Alignment

ORF - retro_ecab_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSKT
          MVQRLTYR.RLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRL.GVRAVRPKVLMRLSKT
Retrocopy MVQRLTYRHRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLQGVRAVRPKVLMRLSKT

Parental  KKHVSRAYGGSMCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQKAK
          KKHVSRAYGGSMCAKCVRDRIK.AFLIEEQKIVVKVLKAQAQSQKAK
Retrocopy KKHVSRAYGGSMCAKCVRDRIKHAFLIEEQKIVVKVLKAQAQSQKAK

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	18.59 RPM	288.71 RPM
SRP021940_cerebellum	11.11 RPM	130.82 RPM
SRP021940_embryo	22.30 RPM	178.11 RPM
SRP021940_placental_villous	8.18 RPM	148.33 RPM
SRP021940_synovial_membrane	13.84 RPM	191.31 RPM
SRP021940_testis	8.18 RPM	114.07 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_58 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_58 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_58 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 163 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009074	10 retrocopies	retro_chof_1313, retro_chof_1474, retro_chof_184, retro_chof_2249, retro_chof_2258, retro_chof_2260, retro_chof_2291, retro_chof_2411, retro_chof_281, retro_chof_324,
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Equus caballus	ENSECAG00000019719	1 retrocopy	retro_ecab_58 ,
Echinops telfairi	ENSETEG00000003715	53 retrocopies	retro_etel_106, retro_etel_107, retro_etel_1125, retro_etel_1140, retro_etel_1182, retro_etel_1187, retro_etel_1232, retro_etel_124, retro_etel_1303, retro_etel_1324, retro_etel_145, retro_etel_1483, retro_etel_1515, retro_etel_1545, retro_etel_1547, retro_etel_158, retro_etel_170, retro_etel_1745, retro_etel_1767, retro_etel_179, retro_etel_1795, retro_etel_1890, retro_etel_1967, retro_etel_1973, retro_etel_2066, retro_etel_2094, retro_etel_217, retro_etel_2191, retro_etel_273, retro_etel_274, retro_etel_299, retro_etel_327, retro_etel_344, retro_etel_362, retro_etel_380, retro_etel_388, retro_etel_416, retro_etel_418, retro_etel_429, retro_etel_464, retro_etel_494, retro_etel_533, retro_etel_726, retro_etel_74, retro_etel_756, retro_etel_759, retro_etel_774, retro_etel_863, retro_etel_870, retro_etel_914, retro_etel_927, retro_etel_938, retro_etel_974,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Myotis lucifugus	ENSMLUG00000000464	4 retrocopies	retro_mluc_125, retro_mluc_1372, retro_mluc_1427, retro_mluc_1847,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Ornithorhynchus anatinus	ENSOANG00000007856	1 retrocopy	retro_oana_92,
Ochotona princeps	ENSOPRG00000001780	11 retrocopies	retro_opri_1013, retro_opri_142, retro_opri_303, retro_opri_311, retro_opri_344, retro_opri_365, retro_opri_39, retro_opri_610, retro_opri_771, retro_opri_907, retro_opri_933,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Sus scrofa	ENSSSCG00000009146	8 retrocopies	retro_sscr_1013, retro_sscr_1014, retro_sscr_1024, retro_sscr_522, retro_sscr_697, retro_sscr_703, retro_sscr_845, retro_sscr_929,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Tursiops truncatus	ENSTTRG00000003443	6 retrocopies