RetrogeneDB ID: retro_ecab_251

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:19055387..19055990(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000017889
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: JOSD1
• Ensembl ID: ENSECAG00000015546
• Aliases: None
• Description: Josephin domain containing 1 [Source:HGNC Symbol;Acc:28953]

Sequence

>retro_ecab_251
ATGAGTTGCAGGCCATGAAAAGGAGACAAGGCCAAACCTGAACTGTTGGAGCTGCCCCAGGCAGCCCCCCCAAATCTACC
ATGAGAAACAGCACAGGGAAACTTTGTGCCCCACGTGCCCTCAGTAACATCTTCCAGGACAATGCCTTCACCTGGGAAAC
GCTCCAAGAGATTTGCCAGAGGTTGTCACCAAACACCGCAGTGAGCCCCCCACAACAAGAGCATGCTGGGAGATGGGAAC
TATGATGTGAACATCATCATGGCAGCACTTCAGACCAAAGGCTATGAAGCTGTGTGGTGGGACAAACGCAGGGATGTCAG
TGCCATTGCTCTGGCTAATGTCGTGGGCTTCGTCATGAATCTGCCCTCCAGCCCGTGCTGGGCTCCCCGGAAGTTGCCTC
TCCAAAGGCAGCACTGGATCTGTGCTCAAGAGGTGGGAGGTGCCTACTACAACCTCAACTCCAAACGGAAGGTGCCCAAG
TGGACCGGAGGCGAGAGCGAGCCCAGGAAATTTCTAGAACACCATTTGCAAGGAAAGAACTATGAATTGCTGCTGGTGGT
AACAGAAGAGGTGGAAGCCCATCAGAGTTGGAGGACTGATGTG

Alignment

ORF - retro_ecab_251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSCVPWKGDKAKSESLELPQAAPPRIYHE-KQRRELCALHALNNVFQDGNAFTRETLQEIFQRLSPNTMV
          MSC.P.KGDKAK.E.LELPQAAPP....E......LCA..AL.N.FQD.NAFT.ETLQEI.QRLSPNT.V
Retrocopy MSCRP*KGDKAKPELLELPQAAPPNLP*E<NSTGKLCAPRALSNIFQD-NAFTWETLQEICQRLSPNTAV

Parental  T-PHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDKRRDVSAIALTNVMGFIMNLPSSLCWGPLKLPLKRQ
          ..PH.KSMLG.GNYDVN.IMAALQTKGYEAVWWDKRRDVSAIAL.NV.GF.MNLPSS.CW.P.KLPL.RQ
Retrocopy S>PHNKSMLGDGNYDVNIIMAALQTKGYEAVWWDKRRDVSAIALANVVGFVMNLPSSPCWAPRKLPLQRQ

Parental  HWICVREVGGAYYNLDSKLKMPEWIGGESELRKFLKHHLRGKNCELLLVVTEEVEAHQSWRTDV
          HWIC..EVGGAYYNL.SK.K.P.W.GGESE.RKFL.HHL.GKN.ELLLVVTEEVEAHQSWRTDV
Retrocopy HWICAQEVGGAYYNLNSKRKVPKWTGGESEPRKFLEHHLQGKNYELLLVVTEEVEAHQSWRTDV

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	13.16 RPM
SRP021940_cerebellum	0.00 RPM	21.86 RPM
SRP021940_embryo	0.10 RPM	18.59 RPM
SRP021940_placental_villous	0.00 RPM	30.45 RPM
SRP021940_synovial_membrane	0.11 RPM	30.64 RPM
SRP021940_testis	0.00 RPM	19.37 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_251 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_251 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_251 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010171	1 retrocopy	retro_btau_1508,
Canis familiaris	ENSCAFG00000001379	1 retrocopy	retro_cfam_1500,
Choloepus hoffmanni	ENSCHOG00000001723	2 retrocopies	retro_chof_1576, retro_chof_233,
Equus caballus	ENSECAG00000015546	1 retrocopy	retro_ecab_251 ,
Felis catus	ENSFCAG00000002821	1 retrocopy	retro_fcat_565,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Microcebus murinus	ENSMICG00000011798	1 retrocopy	retro_mmur_1202,
Myotis lucifugus	ENSMLUG00000003764	1 retrocopy	retro_mluc_1868,
Mus musculus	ENSMUSG00000022426	1 retrocopy	retro_mmus_3014,
Otolemur garnettii	ENSOGAG00000007520	3 retrocopies	retro_ogar_1462, retro_ogar_2911, retro_ogar_3487,
Pteropus vampyrus	ENSPVAG00000010148	1 retrocopy	retro_pvam_181,
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954, retro_rnor_906,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193,
Tarsius syrichta	ENSTSYG00000008846	1 retrocopy	retro_tsyr_1076,