RetrogeneDB ID: retro_ecab_637

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 24:23263460..23264094(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK1
• Ensembl ID: ENSECAG00000009716
• Aliases: None
• Description: cyclin-dependent kinase 1 [Source:HGNC Symbol;Acc:1722]

Sequence

>retro_ecab_637
TCCTTGGATCTTAAGAAATACTTGGATTCTATCCCTCCTGGTCAGTTCATGGATTCTTCACTTATTAAGATTGTCTGTAC
CAAATCCTCCAAGAGATTGTGTTTTATCACCCTAGAAGAGCTCTTCACAGAGACTAACAACCTCAAAACCTATTGATAAC
AAATGAACGATTACTAGCTGATTTTGGCTTTGCCGGAGCTTTTGGAATACCTCTTAGAGTATACACACATGAGGTAGTCA
CTCTCTGCTATAGACCTCCACAAGTATTGCTGGGGTCAACTCACTATTCAACTCCAGTTGACATTTGGAGTCTAGACACC
ATATTTGCAGAATTAGTAACTAAGTAGCCACTTTGCCATGGGGATTCAGAAGTTGATCGACTCTTCAGGATTTTCAGAGC
TTTGGACACCCTCAACAATGAAGCATGGCCGGAAGTGGGATCTTTATAAAATTATAAGAATATGTTTCCCAAGTGGAAAA
CAGGAAGTCCAGCATCTCATGTCAAAAACTTGGTTAAAATGGCTCGGATTTGCTTTCAAAAGTGTTAGTTTATGATCCTG
CCAAACAAGTTGCTGGCAAAATAGCCCTGAACCATCCATGTTTTAATGATTCAGACAATCAGATTAAGAAGATG

Alignment

ORF - retro_ecab_637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.46 %
• Parental protein coverage: 72.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SMDLKKYLDSIPPGQFMDSSLVK-SYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARA
          S.DLKKYLDSIPPGQFMDSSL.K...LYQILQ.IVF.H.RR.LHRD..PQNLLI.......LADFG.A.A
Retrocopy SLDLKKYLDSIPPGQFMDSSLIK<DCLYQILQEIVFYHPRRALHRD*QPQNLLITNERL--LADFGFAGA

Parental  FGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGT
          FGIP.RVYTHEVVTL.YR.P.VLLGS..YSTPVDIWS..TIFAEL.TK.PL.HGDSE.D.LFRIFRAL.T
Retrocopy FGIPLRVYTHEVVTLCYRPPQVLLGSTHYSTPVDIWSLDTIFAELVTK*PLCHGDSEVDRLFRIFRALDT

Parental  PNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDE-NGLDLLSKMLVYDPAKRISGKMALNHPYFNDLD
          .NNE.WPEV.SL..YKN.FPKWK.GS.ASHVKNL...NG.DLLSK.LVYDPAK...GK.ALNHP.FND.D
Retrocopy LNNEAWPEVGSL*NYKNMFPKWKTGSPASHVKNLVK<NGSDLLSKVLVYDPAKQVAGKIALNHPCFNDSD

Parental  NQIKKM
          NQIKKM
Retrocopy NQIKKM

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	0.06 RPM
SRP021940_cerebellum	0.00 RPM	0.21 RPM
SRP021940_embryo	0.00 RPM	14.68 RPM
SRP021940_placental_villous	0.00 RPM	3.95 RPM
SRP021940_synovial_membrane	0.00 RPM	2.88 RPM
SRP021940_testis	0.00 RPM	10.87 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_637 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_637 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671,
Cavia porcellus	ENSCPOG00000005402	3 retrocopies	retro_cpor_1414, retro_cpor_1422, retro_cpor_200,
Dasypus novemcinctus	ENSDNOG00000018590	1 retrocopy	retro_dnov_265,
Equus caballus	ENSECAG00000009716	1 retrocopy	retro_ecab_637 ,
Felis catus	ENSFCAG00000014972	1 retrocopy	retro_fcat_329,
Microcebus murinus	ENSMICG00000005793	1 retrocopy	retro_mmur_43,
Monodelphis domestica	ENSMODG00000017091	1 retrocopy	retro_mdom_702,
Rattus norvegicus	ENSRNOG00000000632	1 retrocopy	retro_rnor_1638,
Tupaia belangeri	ENSTBEG00000017549	3 retrocopies	retro_tbel_3309, retro_tbel_807, retro_tbel_812,
Tursiops truncatus	ENSTTRG00000001085	2 retrocopies	retro_ttru_1619, retro_ttru_1634,