RetrogeneDB ID: retro_ecab_635

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 24:17180503..17180993(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3J
• Ensembl ID: ENSECAG00000008716
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit J [Source:HGNC Symbol;Acc:3270]

Sequence

>retro_ecab_635
AAAAAGAGGTTAGAAGAACCTGAAGAACCTAAAGTGTTAACACCAGAAGAACAATTAGCAGATAAACTCCGGCTAAAGAA
ATTACAGGAAGAGTCAGACCTCGAATTAGCAAAAGAAACTTTTGGTGTTAATAATACAGTTTATGGAATAGATGCTATGA
ACCCATCTTCAAGAGATGACTTCACAGAGTTTGGAAAGTTGTTAAAAGATAAAATTACACAATATGAAAAGTCACTATAT
TATGCCAGTTTTTTGGAAGCCTTAGTTTGAGATGTGTGTATTTCATTGGAAATTGATGACTTGAAAAAGATTACCAATTC
ATTGACTGTGCTTTGCAGTGAAAAACAGAAGCAAGAAAAGCAAAGCAAAGCCAAAAAGAAGAAGAAAGGTGTGGTTCCTG
GAGGGGGGATTAAAGGCCACCATGAAAGACCATCTGGCAGATCATGGTGGTTATGATGGAGGATATGTACAAGACTATGA
AGACTTCATG

Alignment

ORF - retro_ecab_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 77.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKRLEEPEEPKVLTPEEQLADKLRLKKLQEESDLELAKETFGVNNTVYGIDAMNPSSRDDFTEFGKLLKD
          KKRLEEPEEPKVLTPEEQLADKLRLKKLQEESDLELAKETFGVNNTVYGIDAMNPSSRDDFTEFGKLLKD
Retrocopy KKRLEEPEEPKVLTPEEQLADKLRLKKLQEESDLELAKETFGVNNTVYGIDAMNPSSRDDFTEFGKLLKD

Parental  KITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVLCSEKQKQEKQSKAKKKKKGVVPG-GGLKA
          KITQYEKSLYYASFLEALV.DVCISLEIDDLKKITNSLTVLCS.................VVPG.GGLKA
Retrocopy KITQYEKSLYYASFLEALV*DVCISLEIDDLKKITNSLTVLCSXXXXXXXXXXXXXXXXXVVPG>GGLKA

Parental  TMKDDLADYGGYDGGYVQDYEDFM
          TMKD.LAD.GGYDGGYVQDYEDFM
Retrocopy TMKDHLADHGGYDGGYVQDYEDFM

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	2.42 RPM
SRP021940_cerebellum	0.00 RPM	2.60 RPM
SRP021940_embryo	0.08 RPM	5.40 RPM
SRP021940_placental_villous	0.00 RPM	3.27 RPM
SRP021940_synovial_membrane	0.00 RPM	3.02 RPM
SRP021940_testis	0.00 RPM	4.35 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_635 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_635 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Equus caballus	ENSECAG00000008716	1 retrocopy	retro_ecab_635 ,
Homo sapiens	ENSG00000104131	1 retrocopy	retro_hsap_4189,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687, retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Microcebus murinus	ENSMICG00000005006	1 retrocopy	retro_mmur_100,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Otolemur garnettii	ENSOGAG00000004694	1 retrocopy	retro_ogar_1227,