RetrogeneDB ID: retro_ecab_224

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:78868130..78868566(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HLF
• Ensembl ID: ENSECAG00000016953
• Aliases: None
• Description: hepatic leukemia factor [Source:HGNC Symbol;Acc:4977]

Sequence

>retro_ecab_224
CGTCATGACCATAGCCTCCACATTCCCGTAGCCAGCTGCCCAGCTGGCCCTTCTATCCTGGCCCTGACATCTGGGCTCTA
CTCACCCAGCATCCTGTCGCAGAACCGTACACACAATCCCATCAGTCCAGGTCAGCTGCTGTCAGCAAACCACCAGACAT
GGGGCCCATGGATCCTGACAAGATGCAGGTCCCAGTGGGGTACGAGCCAGTTGGGGGAGACCTTGCTCTCTCCAGCATCC
ATGCCCACAAAATATTTGATTCTAGTAAACCCAAGTTCTCTAAGTTTGAACTGAAAGCATAGTCCATGATTAGGAAATCT
CACACAGTCTTCATACCTGGCTGTTGAAATTTAACAAGTACTGAGCTATGATTAGAAAGAACAACACAGCAGCCAAGTGC
TCTTGAGATGCCTGAAGGCTGAGGGAGAAAGAGATT

Alignment

ORF - retro_ecab_224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.63 %
• Parental protein coverage: 58.75 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QHDHSPHPPGLQPASSAAPSVMDLSSRASAPIHPGIPSPNCMQSPIRPGQLLPANRNT-PSPIDPDTIQV
          .HDHS.H.P.......A.PS...L....S....P.I.S.N....PI.PGQLL.AN..T...P.DPD..QV
Retrocopy RHDHSLHIP--VASCPAGPSILALT---SGLYSPSILSQNRTHNPISPGQLLSANHQT<MGPMDPDKMQV

Parental  PVGYEPDPADLALSSIPGQEMFDPRKRKFSEEELKPQPMIKKARKVFIPDD-LKDDKYWARRRKNNMAAK
          PVGYEP...DLALSSI.....FD..K.KFS..ELK...MI.K...VFIP...LK..KY.A..RKNN.AAK
Retrocopy PVGYEPVGGDLALSSIHAHKIFDSSKPKFSKFELKA*SMIRKSHTVFIPGC<LKFNKY*AMIRKNNTAAK

Parental  RSRDARRLKENQI
          .S.DA.RL.E..I
Retrocopy CS*DA*RLREKEI

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	37.01 RPM
SRP021940_cerebellum	0.00 RPM	50.06 RPM
SRP021940_embryo	0.00 RPM	2.40 RPM
SRP021940_placental_villous	0.00 RPM	1.49 RPM
SRP021940_synovial_membrane	0.00 RPM	4.15 RPM
SRP021940_testis	0.00 RPM	1.66 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_224 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_224 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016953	1 retrocopy	retro_ecab_224 ,
Tursiops truncatus	ENSTTRG00000007194	1 retrocopy	retro_ttru_302,