RetrogeneDB ID: retro_ecab_784

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:36656546..36657083(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000016592
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSECAG00000012780
• Aliases: None
• Description: chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]

Sequence

>retro_ecab_784
ATGGCCTTCAATAAAACTATGTTGCAAAAAATGGGAAAGAAACAGAATGGAAAGAGTAAAAAAATTGAAGAGGCAGAGCC
TGAAGAATTTGTATTGGAAAAAGCACAGGACCGATATGTAGTGGATGGGAAGGCGGAATGTTTCCTGAAGTGGAAGGTAA
TACAGACTCTGACAATATTGGGAACCTGAAGAAAGTGTCAATTGTCCAGAGTTAATTGAAATATTTATTAATTCTCAAAG
AACTGGTAAAGAAAAAGGTGGTACAAAAATCTTTATCTGACAGTGAATCTTATGATAGCAAATCAAAGACAAGAGATGTT
GCTGACAAATCAAGAAGCTTTGCCCGAGATCGTGATCCCGAAGAGAATAATGAGTGCCTCACAGAGCAGTGGAGGATTAA
TGTTTCTCAGGAAACGCAAAGATGCCGATGAGGTAGGCTTGGTGCTGGCAAAAGAGGCAAATATGTGGTGTTCCCACATT
GTAACTCCTTTTTATGAAGAGAGACGAACTTGGCATTCCTGCCTGGAAAATGAAGCT

Alignment

ORF - retro_ecab_784 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.75 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWK-GFTDADNT-WEPEENLD
          MA.NKT.L..............EEAEPEEFV.EK..DR.VV.GK.E.FLKWK.G.TD.DN..WEPEE...
Retrocopy MAFNKTMLXXXXXXXXXXXXXXEEAEPEEFVLEKAQDRYVVDGKAECFLKWK<GNTDSDNI<WEPEESVN

Parental  CPELIEAFLNSQKAGKEKDGT-KRKSLSDSESDDSKSKKKRDTADKPRGFARGLDPE-RIIGATDSSGEL
          CPELIE.F.NSQ..GKEK.GT.K..S.S.S....SK....RD.ADK.R.FAR..DPE.RI..A..SSG.L
Retrocopy CPELIEIFINSQRTGKEKGGT>KSLSDSESYDSKSKT---RDVADKSRSFARDRDPE>RIMSASQSSGGL

Parental  MFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEA
          MFL.K.KD.DE..LVLAKEANM.C..IV..FYEER.TWHSC.E.EA
Retrocopy MFLRKRKDADEVGLVLAKEANMWCSHIVTPFYEERRTWHSCLENEA

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	16.29 RPM
SRP021940_cerebellum	0.00 RPM	12.41 RPM
SRP021940_embryo	0.00 RPM	28.13 RPM
SRP021940_placental_villous	0.00 RPM	12.89 RPM
SRP021940_synovial_membrane	0.00 RPM	10.60 RPM
SRP021940_testis	0.00 RPM	10.93 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_784 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_784 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_784 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002897	11 retrocopies	retro_cfam_1157, retro_cfam_161, retro_cfam_1811, retro_cfam_1823, retro_cfam_1849, retro_cfam_2083, retro_cfam_502, retro_cfam_594, retro_cfam_739, retro_cfam_931, retro_cfam_948,
Callithrix jacchus	ENSCJAG00000007952	8 retrocopies	retro_cjac_1100, retro_cjac_1414, retro_cjac_1612, retro_cjac_2405, retro_cjac_2623, retro_cjac_2728, retro_cjac_3322, retro_cjac_869,
Equus caballus	ENSECAG00000012780	1 retrocopy	retro_ecab_784 ,
Loxodonta africana	ENSLAFG00000006907	3 retrocopies	retro_lafr_661, retro_lafr_687, retro_lafr_776,
Mus musculus	ENSMUSG00000029836	1 retrocopy	retro_mmus_77,
Otolemur garnettii	ENSOGAG00000016583	1 retrocopy	retro_ogar_136,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Procavia capensis	ENSPCAG00000004904	2 retrocopies	retro_pcap_108, retro_pcap_166,
Rattus norvegicus	ENSRNOG00000011814	2 retrocopies	retro_rnor_120, retro_rnor_301,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,
Tarsius syrichta	ENSTSYG00000008159	6 retrocopies	retro_tsyr_1459, retro_tsyr_1545, retro_tsyr_1552, retro_tsyr_1645, retro_tsyr_203, retro_tsyr_583,
Tursiops truncatus	ENSTTRG00000000711	7 retrocopies	retro_ttru_1238, retro_ttru_1247, retro_ttru_1851, retro_ttru_294, retro_ttru_52, retro_ttru_591, retro_ttru_644,