RetrogeneDB ID: retro_ecab_685

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 28:12642584..12642925(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH
• Ensembl ID: ENSECAG00000026814
• Aliases: None
• Description: cornichon homolog (Drosophila) [Source:HGNC Symbol;Acc:19431]

Sequence

>retro_ecab_685
TTTGATGACCTGAAGATTGATTACAAGAATCCTAAAGACCAGTGTAATACCTTATATCTTCTTTTATTTTCAGAGTACCT
CACCCATGCTTTCTTCTGTGTCATGTCTGTTTGTGCAGCCGAGGGCTGATGATGGGTTTCAATATTCCCTTCTTTGCACA
CCATACTTGTAGGTATGTGAGTAGACCAGTGAAGAGCAGATCAGCACTCTATGACCCTACAAACATCATCAGTGCAGGTA
TTCAAGCATATCGTCAGAAAGAGGGGTGGTGCAAATTAGATTTTTATTTTCTAGCCTTTTTTTACTACCTATATGGTGTG
ATCTATGTTGTGGTGAGCTCT

Alignment

ORF - retro_ecab_685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.83 %
• Parental protein coverage: 88.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FDELKTDYKNPIDQCNTLNPLVLPEYLIHAFFCVMFLCAAEW-LTLGLNMPLLAYHIWRYMSRPVMSGPG
          FD.LK.DYKNP.DQCNTL..L...EYL.HAFFCVM..CAAE..L..G.N.P..A.H..RY.SRPV.S...
Retrocopy FDDLKIDYKNPKDQCNTLYLLLFSEYLTHAFFCVMSVCAAEG<LMMGFNIPFFAHHTCRYVSRPVKSRSA

Parental  LYDPTTIMNADILAYCQKEGWCKLAFYLLAFFYYLYGMIYVLVSS
          LYDPT.I..A.I.AY.QKEGWCKL.FY.LAFFYYLYG.IYV.VSS
Retrocopy LYDPTNIISAGIQAYRQKEGWCKLDFYFLAFFYYLYGVIYVVVSS

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	8.15 RPM
SRP021940_cerebellum	0.00 RPM	11.58 RPM
SRP021940_embryo	0.00 RPM	11.53 RPM
SRP021940_placental_villous	0.00 RPM	16.07 RPM
SRP021940_synovial_membrane	0.00 RPM	11.47 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_685 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_685 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_658

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031178	2 retrocopies	retro_cfam_658, retro_cfam_697,
Callithrix jacchus	ENSCJAG00000007306	1 retrocopy	retro_cjac_103,
Equus caballus	ENSECAG00000026814	1 retrocopy	retro_ecab_685 ,
Nomascus leucogenys	ENSNLEG00000012704	1 retrocopy	retro_nleu_1896,
Otolemur garnettii	ENSOGAG00000024582	1 retrocopy	retro_ogar_2271,
Ochotona princeps	ENSOPRG00000005287	4 retrocopies	retro_opri_198, retro_opri_269, retro_opri_366, retro_opri_894,
Tupaia belangeri	ENSTBEG00000010265	3 retrocopies	retro_tbel_2080, retro_tbel_3728, retro_tbel_572,
Tarsius syrichta	ENSTSYG00000011295	1 retrocopy	retro_tsyr_1540,
Tursiops truncatus	ENSTTRG00000008259	1 retrocopy	retro_ttru_261,