RetrogeneDB ID: retro_ecab_338

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:76392359..76392974(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH13
• Ensembl ID: ENSECAG00000023146
• Aliases: None
• Description: retinol dehydrogenase 13 (all-trans/9-cis) [Source:HGNC Symbol;Acc:19978]

Sequence

>retro_ecab_338
TTGAAGGAAGAGCCTAGACTGGACGTCTTGATCAATAACGCAGGCATCTTTCAGTGCCCTTATATGAAGACCGAAGACGG
GTTTGAGATGCAGTTTGGAGTGAACCATCTGGGGCACTTCCTGCTCACCAATCTTCTCCTTGGACTCCTCAAAAGTTCAG
CTCCCAGCAGGATTGTGGTAGTTTCTTCCAAACTGTATAAATATGGAGACATCAACTTTGAAGACTTGAACAGTGAACAA
AGCTATAATAAAAGCTTTTGTTATAGTCGGAGCAAACTGGCGAACATTCTTTTTACCAGAGAACTAGCCCGCCGCTTGGA
AGGCACAAACGTTACCGTCAATGTGTTACACCCTGGTATTGTGCGGACTAATCTTGGGAGACACATACACATCCCACTGT
TGGTGAAACCACTTTTCAATTTGGTATCATGGGCTTTTTTCAAAACTCCAGCAGAAGGTGCCCAGACTTCAATTTATTTA
GCATCATCACCTGAAGTAGAAGGCGTATCAGGAAAGTACTTTGGGGATTGTAAAGAAGAGGAACTATTGCCCAAAGCTAT
GGATGAGTCTGTTGCAAGAAAACTCTGGGATATCAGTGAAGTCATGGTTGGCATA

Alignment

ORF - retro_ecab_338 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.33 %
• Parental protein coverage: 62.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAEEEQVHVLVNNAAVMRCPHWTTEDGFEMQFGVNYLGHFLLTNLLLDKLKASAPSRIINLSSLAHVAGH
          L.EE....VL.NNA....CP...TEDGFEMQFGVN.LGHFLLTNLLL..LK.SAPSRI...SS.....G.
Retrocopy LKEEPRLDVLINNAGIFQCPYMKTEDGFEMQFGVNHLGHFLLTNLLLGLLKSSAPSRIVVVSSKLYKYGD

Parental  IDFDDLNWEKRKYDTKAAYCQSKLAIVLFTKELSRRLQGTGVTVNALHPGVARTELGRHTGLHSSAFSSF
          I.F.DLN.E...Y.....Y..SKLA..LFT.EL.RRL.GT.VTVN.LHPG..RT.LGRH...H.......
Retrocopy INFEDLNSE-QSYNKSFCYSRSKLANILFTRELARRLEGTNVTVNVLHPGIVRTNLGRH--IHIPLLVKP

Parental  MLGPIFWLLVKSPQLAAQPSTYLAVAEELEGVSGKYFDGLKEKAPAPEAEDEEVARRLWAESAHLVGL
          ......W...K.P...AQ.S.YLA...E.EGVSGKYF...KE....P.A.DE.VAR.LW..S...VG.
Retrocopy LFNLVSWAFFKTPAEGAQTSIYLASSPEVEGVSGKYFGDCKEEELLPKAMDESVARKLWDISEVMVGI

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	2.83 RPM	0.47 RPM
SRP021940_cerebellum	8.62 RPM	1.77 RPM
SRP021940_embryo	6.34 RPM	4.09 RPM
SRP021940_placental_villous	4.33 RPM	7.17 RPM
SRP021940_synovial_membrane	3.84 RPM	3.46 RPM
SRP021940_testis	7.61 RPM	2.49 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_338 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_338 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1576
Pongo abelii	retro_pabe_1972

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003306	1 retrocopy	retro_amel_114,
Equus caballus	ENSECAG00000015001	1 retrocopy	retro_ecab_1059,
Equus caballus	ENSECAG00000023146	1 retrocopy	retro_ecab_338 ,
Ochotona princeps	ENSOPRG00000015998	2 retrocopies	retro_opri_286, retro_opri_524,
Petromyzon marinus	ENSPMAG00000009095	1 retrocopy	retro_pmar_3,
Pongo abelii	ENSPPYG00000010398	1 retrocopy	retro_pabe_1972,
Pan troglodytes	ENSPTRG00000011484	1 retrocopy	retro_ptro_1576,
Sorex araneus	ENSSARG00000003600	1 retrocopy	retro_sara_314,
Tupaia belangeri	ENSTBEG00000016531	1 retrocopy	retro_tbel_1570,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,