RetrogeneDB ID: retro_ecab_85

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:82314724..82315192(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000001424
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000024045
• Aliases: None
• Description: None

Sequence

>retro_ecab_85
AAGGTCTTCAACCCCGACACCGAGTTCCCAGAGTTCAGCCACCGCCTCATCAAGGACCTGGAGAACATGTTCAAACTGTA
CGATGCTGGACGGGACAGCTTCATCGACCTGATGGAACTGAAGCTGATGATGGAGAAGCTGGAGGCTCCCCAGACCCACC
TGGGCCTGAAGAGCATGATCAAGGAGGTGGACGAGGACTTTGATGGCAAACTCAGCTTCCGTGAGTTCTTGCTCATATTC
CACAAGGCCGCAGCAGGGGAGCTCCAGGAGGATAGCGGGCTGATGGCGCTGGCGAAGCTCTCTGAAATCAATGTTGCCCT
GGAGGGCGTCAAAGGTGCCAAGGAAGTCTTTGAAGCCAAGGTCCAAGCCTTGTCCTCTGCCAGTAAGTTTGAAGCTGAGC
TAAAAGCCAAACAAGATGAGAGGAAGCAGGAGGAAGAGAAGAGGAGGCTCCGCCAGGCGGCCTTCTGA

Alignment

ORF - retro_ecab_85 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.12 %
• Parental protein coverage: 91.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YDAGRDGFIDLMELKLMMEKLGAPQTHLGLKSMIKEVDEDFDGKLSFREFLLIFHKAAAGELQEDSGLMA
          YDAGRD.FIDLMELKLMMEKL.APQTHLGLKSMIKEVDEDFDGKLSFREFLLIFHKAAAGELQEDSGLMA
Retrocopy YDAGRDSFIDLMELKLMMEKLEAPQTHLGLKSMIKEVDEDFDGKLSFREFLLIFHKAAAGELQEDSGLMA

Parental  LAKLSEINVALEGVKGAKDFFEAKVQALSSASKFEAELKAEQDERKQEEEKRRLRQAAF
          LAKLSEINVALEGVKGAK..FEAKVQALSSASKFEAELKA.QDERKQEEEKRRLRQAAF
Retrocopy LAKLSEINVALEGVKGAKEVFEAKVQALSSASKFEAELKAKQDERKQEEEKRRLRQAAF

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	1.89 RPM	12.46 RPM
SRP021940_cerebellum	1.61 RPM	9.19 RPM
SRP021940_embryo	0.43 RPM	1.59 RPM
SRP021940_placental_villous	5.05 RPM	27.38 RPM
SRP021940_synovial_membrane	0.58 RPM	4.50 RPM
SRP021940_testis	0.32 RPM	3.20 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_85 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_85 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_85 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003684	1 retrocopy	retro_chof_1298,
Equus caballus	ENSECAG00000024045	1 retrocopy	retro_ecab_85 ,
Macropus eugenii	ENSMEUG00000008640	1 retrocopy	retro_meug_1315,
Monodelphis domestica	ENSMODG00000010573	2 retrocopies	retro_mdom_1492, retro_mdom_211,