RetrogeneDB ID: retro_ecab_903

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:45624440..45624787(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMYND19
• Ensembl ID: ENSECAG00000012412
• Aliases: None
• Description: zinc finger, MYND-type containing 19 [Source:HGNC Symbol;Acc:21146]

Sequence

>retro_ecab_903
GGGGGAGCGGCGTAGGGGAGGCAGTGCTGGGGCCTTTCAGGTGGTGCATCTCAACATCTGGACAATATGCAGCTGGTGCG
GCGGGGCTGGGGGCCCAAAGCAGAAGAGACCTCCAGAAAACAAAGGGAGCAAAGCTTATATTGGCTGGTGATTCATCAGC
TTCCCATGGGCCCGACAGAAGGGCAGTTCCCCACCTGGTACTATAACGCCAACCGGGACGTGGTGGGAGAGGAGAATTCC
TGCACCTACAACAGTGCCATTATGCTCCCTGAACAGTGACTGAGATGTAGCTCCGGGTGTTCAACATCTGCGGGCGCTGC
TAGATGGCCTGGTCCTGGGGCTCCCAG

Alignment

ORF - retro_ecab_903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.98 %
• Parental protein coverage: 57.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGIAPGFQVVHLNAVTVDNRLDNLQLVPWGWRPKAEETSSKQREQSLYWLAIQQLPTDPIEEQFPVLNVT
          GG.A.G.Q...L........LDN.QLV..GW.PKAEETS.KQREQSLYWL.I.QLP..P.E.QFP....T
Retrocopy GGAA*GRQCWGLSG-GASQHLDNMQLVRRGWGPKAEETSRKQREQSLYWLVIHQLPMGPTEGQFP----T

Parental  RYYNANGDVVEEEENSCTY-YECHYPPCTMIEKQLREFNICGRCQVARYCGSQ
          .YYNAN.DVV..EENSCTY...CHY.P.T..E..LR.FNICGRC..A...GSQ
Retrocopy WYYNANRDVV-GEENSCTY<QQCHYAP*TVTEM*LRVFNICGRC*MAWSWGSQ

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	6.97 RPM
SRP021940_cerebellum	0.00 RPM	17.71 RPM
SRP021940_embryo	0.00 RPM	25.67 RPM
SRP021940_placental_villous	0.00 RPM	9.19 RPM
SRP021940_synovial_membrane	0.00 RPM	12.08 RPM
SRP021940_testis	0.00 RPM	72.96 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_903 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_903 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_903 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006644	2 retrocopies	retro_dnov_1389, retro_dnov_1468,
Dipodomys ordii	ENSDORG00000008360	1 retrocopy	retro_dord_390,
Equus caballus	ENSECAG00000012412	1 retrocopy	retro_ecab_903 ,
Echinops telfairi	ENSETEG00000005023	1 retrocopy	retro_etel_1068,
Homo sapiens	ENSG00000165724	1 retrocopy	retro_hsap_1367,
Gorilla gorilla	ENSGGOG00000006875	1 retrocopy	retro_ggor_1065,
Macropus eugenii	ENSMEUG00000011727	1 retrocopy	retro_meug_2010,
Macaca mulatta	ENSMMUG00000019610	1 retrocopy	retro_mmul_2195,
Monodelphis domestica	ENSMODG00000017172	1 retrocopy	retro_mdom_764,
Mus musculus	ENSMUSG00000026974	3 retrocopies	retro_mmus_1433, retro_mmus_2466, retro_mmus_942,
Nomascus leucogenys	ENSNLEG00000009236	1 retrocopy	retro_nleu_1071,
Tursiops truncatus	ENSTTRG00000010812	1 retrocopy	retro_ttru_900,