RetrogeneDB ID: retro_ecab_40

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 24:4193432..4194278(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004449
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000016515
• Aliases: None
• Description: None

Sequence

>retro_ecab_40
ATGGCCGTCAATGTGTACTCCACATCTGTGACCAGTGAGAATCTGAGTCGCCATGATATGCTTGCTTGGGTCAATGACTC
CCTGCACCTCAACTATACCAAGATAGAACAGCTCTGTTCAGGGGCAGCCTACTGCCAGTTCATGGACATGCTCTTCCCTG
GCTGTGTGCACTTGAGGAAGGTAAAGTTCCAGGCCAAGCTAGAGCACGAATATATCCACAACTTCAAGGTGCTGCAAGCA
GCTTTCAAGAAGATGGGTGTTGACAAAATAATTCCTGTAGAGAAATTAGTGAAAGGAAAATTCCAAGATAATTTTGAGTT
TATTCAGTGGTTTAAGAAATTCTTTGACGCAAACTATGATGGAAAGGATTACAACCCTCTGCTGGCGCGGCAGGGCCAGG
ACATAGCGCCACCTCCTAACCCAGGTGATCAGATCTTCAACAAATCCAAGAAACTCATTGGCACAGCAGTTCCACAGAGG
ACGTCCCCCACAGGCCCCAAAAATATGCAGACCTCTGGCCGACTGAGCAATGTGGCCCCACCCTGCATCCTCCGGAAGAA
TCCTCCATCAGCCCGAAATGGCGGCCATGAGACTGATGCCCAAATTCTTGAACTCAACCAGCAGCTATTGGATTTGAAGC
TGACAGTGGATGGACTAGAGAAGGAACGTGACTTCTACTTCAGCAAACTTCGAGACATTGAGCTCATCTGCCAGGAACAC
GAAAGTGAGAACAGCCCTGTCATCTCGGGCATCATTGGCATTCTCTATGCCACTGAGGAAGGATTTGCACCCCCTGAGGA
CGATGAGATTGAGGAACACCAACAAGAAGACCAGGACGAGTACTGA

Alignment

ORF - retro_ecab_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVNVYSTSVTSENLSRHDMLAWVNDSLHLNYTKIEQLCSGAAYCQFMDMLFPGCVHLRKVKFQAKLEHE
          MAVNVYSTSVTSENLSRHDMLAWVNDSLHLNYTKIEQLCSGAAYCQFMDMLFPGCVHLRKVKFQAKLEHE
Retrocopy MAVNVYSTSVTSENLSRHDMLAWVNDSLHLNYTKIEQLCSGAAYCQFMDMLFPGCVHLRKVKFQAKLEHE

Parental  YIHNFKVLQAAFKKMGVDKIIPVEKLVKGKFQDNFEFIQWFKKFFDANYDGKDYNPLLARQGQDVAPPPN
          YIHNFKVLQAAFKKMGVDKIIPVEKLVKGKFQDNFEFIQWFKKFFDANYDGKDYNPLLARQGQD.APPPN
Retrocopy YIHNFKVLQAAFKKMGVDKIIPVEKLVKGKFQDNFEFIQWFKKFFDANYDGKDYNPLLARQGQDIAPPPN

Parental  PGDQIFNKSKKLIGTAVPQRTSPTGPKNMQTSGRLSNVAPPCILRKNPPSARNGGHETDAQILELNQQLL
          PGDQIFNKSKKLIGTAVPQRTSPTGPKNMQTSGRLSNVAPPCILRKNPPSARNGGHETDAQILELNQQLL
Retrocopy PGDQIFNKSKKLIGTAVPQRTSPTGPKNMQTSGRLSNVAPPCILRKNPPSARNGGHETDAQILELNQQLL

Parental  DLKLTVDGLEKERDFYFSKLRDIELICQEHESENSPVISGIIG-LYATEEGFAPPEDDEIEEHQQEDQDE
          DLKLTVDGLEKERDFYFSKLRDIELICQEHESENSPVISGIIG.LYATEEGFAPPEDDEIEEHQQEDQDE
Retrocopy DLKLTVDGLEKERDFYFSKLRDIELICQEHESENSPVISGIIGILYATEEGFAPPEDDEIEEHQQEDQDE

Parental  Y
          Y
Retrocopy Y

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	1.53 RPM	0.89 RPM
SRP021940_cerebellum	12.26 RPM	8.36 RPM
SRP021940_embryo	1.76 RPM	3.17 RPM
SRP021940_placental_villous	1.20 RPM	0.91 RPM
SRP021940_synovial_membrane	0.77 RPM	1.40 RPM
SRP021940_testis	11.70 RPM	7.03 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_40 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_40 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_40 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016515	1 retrocopy	retro_ecab_40 ,
Ictidomys tridecemlineatus	ENSSTOG00000015500	1 retrocopy	retro_itri_147,
Tupaia belangeri	ENSTBEG00000013617	1 retrocopy	retro_tbel_2390,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,