RetrogeneDB ID: retro_ecab_421

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:42933959..42934678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FLOT1
• Ensembl ID: ENSECAG00000022083
• Aliases: None
• Description: flotillin 1 [Source:HGNC Symbol;Acc:3757]

Sequence

>retro_ecab_421
CTGAAGGACACTCATGATCATCAGGACTATTTGCACTCCTTGGGGAAGGCTCTAACTTCTCAAGTCCAAAATGATGTTCC
TATTGGGGAGGTGGATGCCAAGAGAGATGCTGGGATCCAGGAGGCCAAAGCCAAAAAGGAAAAGGTGAGTGCTCAGCACC
TGAGTGAGATGGAGATGACCAAGGGGCAGAGGGACTAGGAGCTGAGAAGGCTGTGTATGACATCAAAGTCACCACCAGCA
GCTTGAGCTGGACTGTCAGCTTCAGGTGGCCAAGACTAAGCAGCAGATGGAGGAAAAGTGGGTACAGATGCAGGTGGTGG
AGCAGGCACAGCAGGTGGCAGTGCAGGAGCCAGAGATCGCACACCGAGAGAAGGAGCTGGAGGTCCGAGTTCTGAAGCCA
GTAGAAGTCTAGTGCTACAAGCTGGAGCACCTAGCTGAGGCAGAAACGTCTCAGCTGATTCTGCAGGCAGACAGAAGCCG
AGTCTGTGCAGATGCGGGAGGATGCCAAGGCTTTGCCACAGAGATTGGAGCTCTGGGTCAAGCTTGAGAAGATGGCCAAG
AAGGCAGAAGAGTTCCAGCAGTACCTGGAGGCTGCTTGGCTGGACATTCTGCTAGAGAAGCTGCCCCAGGTGGCAGAGAT
CAGTGGTACCTTGATCTTGGCCAACAAGATCACATTGGGGTCCAGTGGAAGTGGGGCCGTGGGGGTGGCCAAAATGACC

Alignment

ORF - retro_ecab_421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.37 %
• Parental protein coverage: 57.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKDIHDDQDYLHSLGKARTAQVQKDARIGEAEAKRDAGIREAKAKQEKVSAQYLSEIEMAKAQRDYELK-
          LKD.HD.QDYLHSLGKA.T.QVQ.D..IGE..AKRDAGI.EAKAK.EKVSAQ.LSE.EM.K.QRD.EL..
Retrocopy LKDTHDHQDYLHSLGKALTSQVQNDVPIGEVDAKRDAGIQEAKAKKEKVSAQHLSEMEMTKGQRD*ELR<

Parental  KAAYDIEVNT-RRAQADLAYQLQVAKTKQQIEEQRVQVQVVERAQQVAVQEQEIARREKELEARVRKPAE
          KA.YDI.V.T......D...Q..VAKTKQQ.EE..VQ.QVVE.AQQVAVQE.EIA.REKELE.RV.KP.E
Retrocopy KAVYDIKVTT<QQLELDCQLQ--VAKTKQQMEEKWVQMQVVEQAQQVAVQEPEIAHREKELEVRVLKPVE

Parental  AERYKLERLAEAEKTQLIMQAEAEAESVRMRGEAEAFAIGARARADA-EQMSKKAEAFQLYQEAAQLDML
          ...YKLE.LAEAE..QLI.QA..........G....FA....A...A.E.M.KKAE.FQ.Y.EAA.LD.L
Retrocopy V*CYKLEHLAEAETSQLILQAD-RSRVCADAGGCQGFATEIGALGQA>EKMAKKAEEFQQYLEAAWLDIL

Parental  LEKLPQVAEEISGPLTSAKKITLVSSGSGTMGAAKVT
          LEKLPQVA.EISG.L..A.KITL.SSGSG..G.AK.T
Retrocopy LEKLPQVA-EISGTLILANKITLGSSGSGAVGVAKMT

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	45.16 RPM
SRP021940_cerebellum	0.00 RPM	117.83 RPM
SRP021940_embryo	0.00 RPM	53.32 RPM
SRP021940_placental_villous	0.00 RPM	131.01 RPM
SRP021940_synovial_membrane	0.00 RPM	103.44 RPM
SRP021940_testis	0.00 RPM	19.18 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_421 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_421 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_421 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000022083	1 retrocopy	retro_ecab_421 ,