RetrogeneDB ID: retro_ecab_561

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:5856285..5856653(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC15
• Ensembl ID: ENSECAG00000007757
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 15 [Source:HGNC Symbol;Acc:20325]

Sequence

>retro_ecab_561
ACCACCAGACCCTATGCCAACATTGCCAGGGCCTGGCAAGACAGGGTCAGTAGTGGGATTGGCTGTTGCAGGCTTTGCAG
TTTTGTGTATTTTACAGCTGCATATTTCAAGTCTGGAAAATTCTGCAACAAGTAATCACAGAAAATGTGAAAATTTCAAC
CCCGAGCATTCCATCTTCTTATAAAAAGAATTTAAACAAAAAATGAGTAGGCGTGAAGCTAGACTTATTTTAGGTGTAAG
CCCATCTGCTGGTAAAGCTGGAATTAGAACGGGTCACAGGAAATCATGATTGTGAATTAAGCAGATAACAGGGATTCTCC
TATTTAGCAACCCAAAGATGCAAAGTAGAAATCGTGCTGGATTGAACA

Alignment

ORF - retro_ecab_561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.49 %
• Parental protein coverage: 82.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  TRRPDADID-QGLAR-SLIAVGLGVA-ALAFAGRYA--FQIWKPLEQVITDAAKKISVQSLSSYYKGG-F
          T.RP.A.I..QGLAR.....VGL.VA.AL.F...Y...FQ.WK.L.QVIT...K.IS..S..S.YK...F
Retrocopy TTRPYANIA<QGLAR<TGSVVGLAVA>ALQFCVFYSCIFQVWKILQQVITENVK-ISTPSIPSSYKKN<F

Parental  EQKMSRREASLILGVSPSAGKAKIRTAHRR-IMILNHPDKGGSP-YLATKINEAKDLLEAT
          .QKMSRREA.LILGVSPSAGKA.IRT.HR..IMI.N..D...SP.YLAT........L..T
Retrocopy KQKMSRREARLILGVSPSAGKAGIRTGHRK<IMIVN*ADNRDSP<YLATQRCKVEIVLD*T

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	1.83 RPM
SRP021940_cerebellum	0.00 RPM	3.69 RPM
SRP021940_embryo	0.00 RPM	3.17 RPM
SRP021940_placental_villous	0.00 RPM	14.10 RPM
SRP021940_synovial_membrane	0.00 RPM	2.64 RPM
SRP021940_testis	0.00 RPM	27.62 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_561 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_561 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_561 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3331
Pan troglodytes	retro_ptro_2148
Gorilla gorilla	retro_ggor_1294
Oryctolagus cuniculus	retro_ocun_487
Canis familiaris	retro_cfam_939

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034785	1 retrocopy	retro_btau_1624,
Canis familiaris	ENSCAFG00000004664	1 retrocopy	retro_cfam_939,
Callithrix jacchus	ENSCJAG00000017589	2 retrocopies	retro_cjac_1663, retro_cjac_634,
Cavia porcellus	ENSCPOG00000003485	1 retrocopy	retro_cpor_327,
Equus caballus	ENSECAG00000007757	1 retrocopy	retro_ecab_561 ,
Erinaceus europaeus	ENSEEUG00000008785	5 retrocopies	retro_eeur_360, retro_eeur_608, retro_eeur_64, retro_eeur_93, retro_eeur_95,
Felis catus	ENSFCAG00000022632	1 retrocopy	retro_fcat_259,
Homo sapiens	ENSG00000120675	2 retrocopies	retro_hsap_3331, retro_hsap_4312,
Gorilla gorilla	ENSGGOG00000016338	2 retrocopies	retro_ggor_1294, retro_ggor_2882,
Loxodonta africana	ENSLAFG00000004343	2 retrocopies	retro_lafr_287, retro_lafr_942,
Myotis lucifugus	ENSMLUG00000008684	3 retrocopies	retro_mluc_1358, retro_mluc_1544, retro_mluc_520,
Macaca mulatta	ENSMMUG00000013689	1 retrocopy	retro_mmul_1169,
Mustela putorius furo	ENSMPUG00000001704	1 retrocopy	retro_mputfur_1065,
Nomascus leucogenys	ENSNLEG00000001759	4 retrocopies	retro_nleu_1408, retro_nleu_1464, retro_nleu_1675, retro_nleu_585,
Oryctolagus cuniculus	ENSOCUG00000001696	4 retrocopies	retro_ocun_1101, retro_ocun_487, retro_ocun_882, retro_ocun_936,
Ochotona princeps	ENSOPRG00000016191	5 retrocopies	retro_opri_1038, retro_opri_235, retro_opri_285, retro_opri_756, retro_opri_766,
Pongo abelii	ENSPPYG00000005323	1 retrocopy	retro_pabe_3508,
Pan troglodytes	ENSPTRG00000005831	2 retrocopies	retro_ptro_2148, retro_ptro_2920,
Pteropus vampyrus	ENSPVAG00000011281	1 retrocopy	retro_pvam_807,
Sorex araneus	ENSSARG00000007683	1 retrocopy	retro_sara_658,
Ictidomys tridecemlineatus	ENSSTOG00000012805	1 retrocopy	retro_itri_1710,
Taeniopygia guttata	ENSTGUG00000012364	2 retrocopies	retro_tgut_20, retro_tgut_45,
Tursiops truncatus	ENSTTRG00000015580	1 retrocopy	retro_ttru_1021,
Vicugna pacos	ENSVPAG00000001445	1 retrocopy	retro_vpac_113,