RetrogeneDB ID: retro_ecab_415

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:37294712..37295285(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOLR4
• Ensembl ID: ENSECAG00000007254
• Aliases: None
• Description: folate receptor 4, delta (putative) [Source:HGNC Symbol;Acc:32565]

Sequence

>retro_ecab_415
AATGCCTGCTGCAGGGCTATCACCATGGGGGAAGCCCACCTGGATGTGTCCCTGCTCTACAACTTCATATTGGTCCATTG
TGGATTGATGACCTGGGCCTGTCAAAAGCACTTCGTCCAGGCCGCCTAGTTCTACGGGTGCTCCCGGAACCTGGGGCCTT
GGATCCAGCGCGTGACCCCGAGTGGGCAGGCAGAGCGAATTTTGGATGAGCCCCTCTGCCTGGAGGACCGTGAGTAGTGG
TGCGCAGGCTGCCGCTCATCTTACACTTGCAAATCCAGTGGGCAAGGCGCCTGCGACCGGAGTCGGGTGAACAACTGCTG
CCCTACAAGGGCCCAGTGCCACTCTTTTCCCCCGTTACTACTCCACCCTCGCTGACCTGTGCGAGAAGATTTGGAGCAAC
TCCTTCAAGGTGAGCCCTGAGCACCGCAACAGGGGGCGGTACTTCCAGAAGTGGGTGAGCCTGCTCAGGGCAGCCCCAGT
GAGGCTAGGACCCGCCCCTTCGCCAGCCCTTCCCCGTTCTGGCAAATTCCCAACATTCTATTGGCCTTCTCTCTGTTCCT
GTTATTCCTTTCC

Alignment

ORF - retro_ecab_415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.73 %
• Parental protein coverage: 78.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SACCTANTSWKAHLNVSLLYNFSLVHCGLMMPGCQRHFIQAVCFYECSPNLGPWIQQVDLSGQGERILDA
          .ACC.A.T...AHL.VSLLYNF.LVHCGLM...CQ.HF.QA..FY.CS.NLGPWIQ.V..SGQ.ERILD.
Retrocopy NACCRAITMGEAHLDVSLLYNFILVHCGLMTWACQKHFVQAA*FYGCSRNLGPWIQRVTPSGQAERILDE

Parental  PLCREDCEQWWEDCRTSYTCKSNWHGGWDWSGGKNRCPARARCHP-FPHYFPTPADLCERIWSNSFKASP
          PLC.ED.E.W...CR.SYTCKS...G..D.S...N.CP.RA.CH..FP.Y..T.ADLCE.IWSNSFK.SP
Retrocopy PLCLEDRE*WCAGCRSSYTCKSSGQGACDRSRVNNCCPTRAQCHS>FPRYYSTLADLCEKIWSNSFKVSP

Parental  EHRNSGRCLQKWF-EPAQGNPNEAVARLFASPAWSWEFSHTLMAFSLFLSCLS
          EHRN.GR..QKW..EPAQG.P.EA..R.FASP...W.....L.AFSLFL..LS
Retrocopy EHRNRGRYFQKWV<EPAQGSPSEARTRPFASPSPFWQIPNILLAFSLFLLFLS

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	0.59 RPM
SRP021940_cerebellum	0.00 RPM	0.05 RPM
SRP021940_embryo	0.00 RPM	0.26 RPM
SRP021940_placental_villous	0.00 RPM	0.00 RPM
SRP021940_synovial_membrane	0.00 RPM	0.30 RPM
SRP021940_testis	0.00 RPM	11.89 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_415 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_415 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_282

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011928	2 retrocopies	retro_amel_1133, retro_amel_1192,
Equus caballus	ENSECAG00000007254	1 retrocopy	retro_ecab_415 ,
Loxodonta africana	ENSLAFG00000032394	1 retrocopy	retro_lafr_913,
Sus scrofa	ENSSSCG00000014952	1 retrocopy	retro_sscr_282,