RetrogeneDB ID: retro_ecab_406

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:10133507..10133848(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL30
• Ensembl ID: ENSECAG00000021705
• Aliases: None
• Description: ribosomal protein L30 [Source:HGNC Symbol;Acc:10333]

Sequence

>retro_ecab_406
ATAGTGGCCAAAAAGAAGAGGCAAAAGTTGCTAGAGTCCATCAACTCTAGGCCCCAACTGATTATGAACAGCGGAAAGTC
GATGCTTGGTACAAGCCACCTCTGAAGATGATACTCAAAGCAAAGCAAAACTGGTCATCCTTGCCAAAACCGCCCGACGG
CGAGGAAATCTGAAATAGAGTCCTATGCCACGTCGGCCCAAACCGGTGTCCAGCACTACAGGGCAATAACATTGAACCGG
GCACAGCACGCAGGAAAGACGACAGAGTATGCACACTGGCTGTCATTGGTCCAGGTGGTTCTGTGACCTTTAGAAGTGTG
CCAGAATAGACTGGTAAAAAG

Alignment

ORF - retro_ecab_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MVAAKKTKKSLESINSRLQLVMKSGKYVLG-YKQTLKMI-RQGKAKLVILAN-NCPALRKSEIEYYAMLA
          .VA.KK..K.LESINSR.QL.M.SGK..LG.YK..LKMI..Q.KAKLVILA..N.P..RKSEIE.YA..A
Retrocopy IVAKKKRQKLLESINSRPQLIMNSGKSMLG<YKPPLKMI<TQSKAKLVILAK<NRPTARKSEIESYATSA

Parental  KTGVHHY-SGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQTGEK
          .TGV.HY..GNNIE.GTA..K..RVCTLA.I.PG.S...RS.PE.TG.K
Retrocopy QTGVQHY<QGNNIEPGTARRKDDRVCTLAVIGPGGSVTFRSVPE*TGKK

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	441.01 RPM
SRP021940_cerebellum	0.00 RPM	187.32 RPM
SRP021940_embryo	0.00 RPM	351.01 RPM
SRP021940_placental_villous	0.19 RPM	162.81 RPM
SRP021940_synovial_membrane	0.63 RPM	254.45 RPM
SRP021940_testis	0.00 RPM	157.81 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_406 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_406 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 160 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016047	2 retrocopies	retro_acar_170, retro_acar_47,
Ailuropoda melanoleuca	ENSAMEG00000000605	18 retrocopies	retro_amel_1007, retro_amel_1148, retro_amel_1205, retro_amel_1456, retro_amel_1490, retro_amel_1596, retro_amel_1709, retro_amel_1738, retro_amel_26, retro_amel_384, retro_amel_40, retro_amel_456, retro_amel_50, retro_amel_534, retro_amel_551, retro_amel_642, retro_amel_745, retro_amel_806,
Bos taurus	ENSBTAG00000016278	2 retrocopies	retro_btau_34, retro_btau_992,
Callithrix jacchus	ENSCJAG00000015549	4 retrocopies	retro_cjac_14, retro_cjac_253, retro_cjac_320, retro_cjac_351,
Cavia porcellus	ENSCPOG00000026030	4 retrocopies	retro_cpor_1287, retro_cpor_1325, retro_cpor_505, retro_cpor_764,
Dasypus novemcinctus	ENSDNOG00000013828	12 retrocopies	retro_dnov_1331, retro_dnov_1754, retro_dnov_1883, retro_dnov_2094, retro_dnov_2208, retro_dnov_2455, retro_dnov_2484, retro_dnov_2513, retro_dnov_2670, retro_dnov_293, retro_dnov_334, retro_dnov_415,
Dipodomys ordii	ENSDORG00000012383	10 retrocopies	retro_dord_111, retro_dord_204, retro_dord_361, retro_dord_407, retro_dord_49, retro_dord_69, retro_dord_710, retro_dord_736, retro_dord_83, retro_dord_97,
Equus caballus	ENSECAG00000021705	7 retrocopies	retro_ecab_1094, retro_ecab_227, retro_ecab_406 , retro_ecab_508, retro_ecab_599, retro_ecab_63, retro_ecab_945,
Erinaceus europaeus	ENSEEUG00000000964	9 retrocopies	retro_eeur_137, retro_eeur_214, retro_eeur_237, retro_eeur_355, retro_eeur_432, retro_eeur_59, retro_eeur_614, retro_eeur_69, retro_eeur_83,
Felis catus	ENSFCAG00000002165	9 retrocopies	retro_fcat_1261, retro_fcat_1391, retro_fcat_1473, retro_fcat_1689, retro_fcat_1872, retro_fcat_323, retro_fcat_45, retro_fcat_49, retro_fcat_754,
Homo sapiens	ENSG00000156482	9 retrocopies	retro_hsap_1104, retro_hsap_1947, retro_hsap_2229, retro_hsap_2767, retro_hsap_3509, retro_hsap_3959, retro_hsap_4000, retro_hsap_4652, retro_hsap_475,
Loxodonta africana	ENSLAFG00000002077	2 retrocopies	retro_lafr_122, retro_lafr_882,
Microcebus murinus	ENSMICG00000004620	3 retrocopies	retro_mmur_258, retro_mmur_644, retro_mmur_693,
Myotis lucifugus	ENSMLUG00000003637	11 retrocopies	retro_mluc_1425, retro_mluc_2001, retro_mluc_2274, retro_mluc_2295, retro_mluc_2409, retro_mluc_409, retro_mluc_583, retro_mluc_639, retro_mluc_827, retro_mluc_838, retro_mluc_894,
Macaca mulatta	ENSMMUG00000020073	12 retrocopies	retro_mmul_1353, retro_mmul_2275, retro_mmul_2291, retro_mmul_2309, retro_mmul_2322, retro_mmul_2473, retro_mmul_29, retro_mmul_319, retro_mmul_416, retro_mmul_576, retro_mmul_663, retro_mmul_857,
Monodelphis domestica	ENSMODG00000006804	1 retrocopy	retro_mdom_664,
Oryctolagus cuniculus	ENSOCUG00000017386	4 retrocopies	retro_ocun_1447, retro_ocun_1580, retro_ocun_178, retro_ocun_279,
Ochotona princeps	ENSOPRG00000007644	3 retrocopies	retro_opri_1087, retro_opri_662, retro_opri_954,
Pan troglodytes	ENSPTRG00000020454	10 retrocopies	retro_ptro_1146, retro_ptro_1302, retro_ptro_1575, retro_ptro_1874, retro_ptro_2334, retro_ptro_2380, retro_ptro_2688, retro_ptro_3091, retro_ptro_356, retro_ptro_693,
Pteropus vampyrus	ENSPVAG00000014461	9 retrocopies	retro_pvam_1079, retro_pvam_1090, retro_pvam_1099, retro_pvam_161, retro_pvam_276, retro_pvam_279, retro_pvam_407, retro_pvam_506, retro_pvam_561,
Rattus norvegicus	ENSRNOG00000005975	19 retrocopies	retro_rnor_1, retro_rnor_1038, retro_rnor_1631, retro_rnor_1812, retro_rnor_1830, retro_rnor_1876, retro_rnor_1893, retro_rnor_1946, retro_rnor_1975, retro_rnor_2211, retro_rnor_2598, retro_rnor_2636, retro_rnor_2666, retro_rnor_2736, retro_rnor_739, retro_rnor_745, retro_rnor_753, retro_rnor_761, retro_rnor_940,