RetrogeneDB ID: retro_ecab_795

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:88945278..88945957(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC10A7
• Ensembl ID: ENSECAG00000026901
• Aliases: None
• Description: solute carrier family 10 (sodium/bile acid cotransporter family), member 7 [Source:HGNC Symbol;Acc:23088]

Sequence

>retro_ecab_795
GCAGCTGCACTATTTAATTCAGCCTTTGGAAGTTTTTTGGGCATCGTTATAACACCCTTACTATTGCTGCTTTTTCTTGG
CTCATCCTCTTCTGTGCCTTTTACATCTATTTTTTCTCAGCTTTTTATAACTGTTGTGGTTCCTCTCATTATTGGACAGA
TTGTCCGAAGATACATCAAGGATTGGCTTGAAAGAAAGAAACTGCCTTTTGGTGCTATCAGCAGCAGTAGGCTCCTCATG
ATCATCTACACGACATTCTGTGACACGTTCTCTAACCCAAATATTGACCTGGATAAATTCAGCCTTATTCTCATACTGTT
CATAATATTTTCTATTCAGCTGAGTTTTATGCTTTTAACCTTCATCTTTTCAACCAGGAATAATTCGGGTTTCACACCAG
CAGACACCGTGGCTATCATTTTCTGTTCTACACACAAATCCCTCACGTTAGGGATTCCAATGCTGAAGATAGTGTTTGCA
GGCCAAGAGCACCTCCCGTTGATATCTGTCCCCCTGCTCATCTACCATCCGGTTCAGATCCTGCTGGGCAGTGTGCTGGT
GCCAACAATAAAGTCTTGGATGGTGTCAAGGCAGAAGAAACTGCTCCAAACCAGGGGACCACTGGCTAACTTAGAATAAT
CCAGAAGACTTGGAATATTTATCTATCCCACTTGACCAC

Alignment

ORF - retro_ecab_795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.51 %
• Parental protein coverage: 63.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAAIFNSAFGSFLGIVITPLLLLLFLGSSSSVPFTSIFSQLFMTVVVPLIIGQIVRRYIKDWLERKKPPF
          AAA.FNSAFGSFLGIVITPLLLLLFLGSSSSVPFTSIFSQLF.TVVVPLIIGQIVRRYIKDWLERKK.PF
Retrocopy AAALFNSAFGSFLGIVITPLLLLLFLGSSSSVPFTSIFSQLFITVVVPLIIGQIVRRYIKDWLERKKLPF

Parental  GAISSSVLLMIIYTTFCDTFSNPNIDLDKFSLILILFIIFSIKICPMYY-FIVRSRNNSGFTPADTVAII
          GAISSS.LLMIIYTTFCDTFSNPNIDLDKFSLILILFIIFSI....M...FI...RNNSGFTPADTVAII
Retrocopy GAISSSRLLMIIYTTFCDTFSNPNIDLDKFSLILILFIIFSIQLSFMLLTFIFSTRNNSGFTPADTVAII

Parental  FCSTHKSLTLGIPMLKIVFAGHEHLSLISVPLLIYHPVQILLGSVLVPTIKSWMVSRQKKLLQTRGPLAN
          FCSTHKSLTLGIPMLKIVFAG.EHL.LISVPLLIYHPVQILLGSVLVPTIKSWMVSRQKKLLQTRGPLAN
Retrocopy FCSTHKSLTLGIPMLKIVFAGQEHLPLISVPLLIYHPVQILLGSVLVPTIKSWMVSRQKKLLQTRGPLAN

Parental  L-NNPEDLEYLSIPLDH
          L.NNPEDLEYLSIPLDH
Retrocopy L>NNPEDLEYLSIPLDH

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	0.06 RPM	1.36 RPM
SRP021940_cerebellum	0.05 RPM	0.83 RPM
SRP021940_embryo	0.03 RPM	1.66 RPM
SRP021940_placental_villous	0.00 RPM	1.64 RPM
SRP021940_synovial_membrane	0.03 RPM	1.37 RPM
SRP021940_testis	0.00 RPM	2.75 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_795 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_795 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_795 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000026901	1 retrocopy	retro_ecab_795 ,