RetrogeneDB ID: retro_ecab_181

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:110345945..110346358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPK
• Ensembl ID: ENSECAG00000019165
• Aliases: None
• Description: centromere protein K [Source:HGNC Symbol;Acc:29479]

Sequence

>retro_ecab_181
TCAGTGAATCAGCAAGATATCTATCCAGACAGCACTACAGATGCAGAAGATGTTAAGTTGTTGAAGAAGAACTCACGAAA
GAATGTAAAGAAACATGGAATGATATGGAAGAATGTCAGAATCAATTATCTCTTCTTGGAACTGAGACACTCACTGATTC
AAATGCTCAGTTATCATTGTTAACTCTGCAAGTAAAATATCTGACCACCGAATTCAGTTAATGGTAGAAAGAAACTCCTG
AAATAATTCCACTGAATGAAGATGTTCTGGTAGCGTTAGGAAAAGGAGAGTTCCAAAAACTGAGATATGATCTTGAAATG
GCACTTTCTACTATTCAGTCAAAGAATGGAAAGTTACAGGAAGACTTGGAAACAGAATAACAATGGTTAGATGAACAGCA
ATAGATACTGGAA

Alignment

ORF - retro_ecab_181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.66 %
• Parental protein coverage: 50.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVNQQDLDPDSTTEVEDVT-DAEEELIKECEELWKDMEECQNKLSLVGTETLTESNAQLSLLIMQMKCLT
          SVNQQD..PDSTT..EDV....EEEL.KEC.E.W.DMEECQN.LSL.GTETLT.SNAQLSLL..Q.K.LT
Retrocopy SVNQQDIYPDSTTDAEDVK<VVEEELTKECKETWNDMEECQNQLSLLGTETLTDSNAQLSLLTLQVKYLT

Parental  AELSQWQKETPKIIPLNEEVLLTLGKEEFQKLRHDLELVLSTIQSKNEKLKEDLEREQQWLKEQQQLLE
          .E.S.W.KETP.IIPLNE.VL..LGK.EFQKLR.DLE..LSTIQSKN.KL.EDLE.E.QWL.EQQ..LE
Retrocopy TEFS*W*KETPEIIPLNEDVLVALGKGEFQKLRYDLEMALSTIQSKNGKLQEDLETE*QWLDEQQ*ILE

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.16 RPM
SRP021940_embryo	0.00 RPM	4.45 RPM
SRP021940_placental_villous	0.00 RPM	0.19 RPM
SRP021940_synovial_membrane	0.00 RPM	0.55 RPM
SRP021940_testis	0.00 RPM	1.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_181 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_181 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013993	1 retrocopy	retro_chof_1252,
Dipodomys ordii	ENSDORG00000007357	1 retrocopy	retro_dord_787,
Equus caballus	ENSECAG00000019165	1 retrocopy	retro_ecab_181 ,
Erinaceus europaeus	ENSEEUG00000005831	1 retrocopy	retro_eeur_81,
Monodelphis domestica	ENSMODG00000019645	1 retrocopy	retro_mdom_1446,
Oryctolagus cuniculus	ENSOCUG00000011568	2 retrocopies	retro_ocun_1199, retro_ocun_74,
Tursiops truncatus	ENSTTRG00000006527	1 retrocopy	retro_ttru_1310,