RetrogeneDB ID: retro_ecab_148

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:138424661..138425569(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT4
• Ensembl ID: ENSECAG00000016982
• Aliases: None
• Description: chaperonin containing TCP1, subunit 4 (delta) [Source:HGNC Symbol;Acc:1617]

Sequence

>retro_ecab_148
GTGGCTAATTCTGACAAAACCAGAGTTGAAAAGACTAAGATTGGGCTTATTCAGTTTAGCTTATCTGCTCCCAGAACAGA
TATGGATAATCAAACAGTAATTTCTGATATGCCCGGATGGACTGAGCGCTTCGAGAGGAGAGAGCCTGCATTCTATATTT
AGTGAACCAAATTTTAAAAACAGGATATAGTATGCTTCTCATATAGAAGTCTATTCTTAAGAGAGGCTCTTAGTGATCTT
TCATGACATCTCATTAACAAAATGAAGATGATGGTTAAGGATACGGAAAATGAAGACGTTGAAGTTGTTTGTAAGACAGT
TGGAACCAACCCAGTTGCTCATTTTGACCAATTCACTCCTGACCTGCTGGGTTTGGCTGAGTTAGCTGAGGGGGTCCATT
TAAATGGTTCTGGCAAACTACTCAAGGTTACAGGCTGCGCACGCCCTGGAAAAAGTTACAGTTGCTGTTCGTGGTTCTAA
AAAATTGGTGATTGAAGAAGCTGAGCGCTCCATTCACGACGCGTGATGTGTTATTCGCTGTTTAGTGAAGAGGAGAGCTC
TTATTGCATGACATGGTGTGCCAGAACTAGAGTTGGCCCTGTGGTTAACTGAGTATTCATGAACATTGAGTGGATGGGAT
CCTGCTGCGTTCGTGCCTTTGCAGGTGTTATGGAGGTCATTCTACCGACGCTATCTGAAACTGCTGGCCTGAGTCCCGTT
TCTGCAGTAACAGAACTAAGGAACTGGCATGCCCAGAGAGAAAAACTACAGGCATTAATGTCCAAAAGGATGGTATTTCC
AGTGTTTTGGAGGAACTGGTTGTCCAGCCTTTGTTGGTTTCAGTCAGTGTGCTGACTCTAGCAACTGATACTGTCTGGAT
CAGTCTGCAAATTGATGATGTGGTAAAC

Alignment

ORF - retro_ecab_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 61.37 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VANSGITRVEKAKIGLIQFCLSAPKTDMDNQIVVSD-YVQMDRVLREERAYILNLVKQIKKTGCNVLLIQ
          VANS..TRVEK.KIGLIQF.LSAP.TDMDNQ.V.SD.Y..MD..LREERA.IL.LV.QI.KTG...LLI.
Retrocopy VANSDKTRVEKTKIGLIQFSLSAPRTDMDNQTVISD<YARMD*ALREERACILYLVNQILKTGYSMLLI*

Parental  KSIL-RDALSDLALHFLNKMKIMVVKDIEREDIEFICKTIGTKPVAHIDQFTADMLGSAELAEEVNLNGS
          KSIL.R.ALSDL..H..NKMK.MV.KD.E.ED.E..CKT.GT.PVAH.DQFT.D.LG.AELAE.V.LNGS
Retrocopy KSIL>REALSDLS*HLINKMKMMV-KDTENEDVEVVCKTVGTNPVAHFDQFTPDLLGLAELAEGVHLNGS

Parental  GKLLKITGCT-SPGKT-VTIVVRGSNKLVIEEAERSIHDALCVIRCLVKKRALIAGGGAPEIELALRLTE
          GKLLK.TGC...P.K..VT..VRGS.KLVIEEAERSIHDA.CVIRCLVK.RALIA..G.PE.ELAL.LTE
Retrocopy GKLLKVTGCA<TPWKK<VTVAVRGSKKLVIEEAERSIHDA*CVIRCLVKRRALIA*HGVPELELALWLTE

Parental  YSRTLSG-MESYCVRAFADAMEVIPSTLAENAGLNPISTVTELRNRHAQGE-KTTGINVRKGGISNILEE
          YS.TLSG.M.S.CVRAFA..MEVI..TL.E.AGL.P.S.VTELRN.HAQ.E.KTTGINV.K.GIS..LEE
Retrocopy YS*TLSG<MGSCCVRAFAGVMEVILPTLSETAGLSPVSAVTELRNWHAQRE<KTTGINVQKDGISSVLEE

Parental  LVVQPLLVSVSALTLATETVRSILKIDDVVN
          LVVQPLLVSVS.LTLAT.TV...L.IDDVVN
Retrocopy LVVQPLLVSVSVLTLATDTVWISLQIDDVVN

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	29.46 RPM
SRP021940_cerebellum	0.00 RPM	91.04 RPM
SRP021940_embryo	0.00 RPM	103.29 RPM
SRP021940_placental_villous	0.00 RPM	58.21 RPM
SRP021940_synovial_membrane	0.00 RPM	51.66 RPM
SRP021940_testis	0.00 RPM	189.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_148 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_148 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003083	2 retrocopies	retro_cfam_2093, retro_cfam_590,
Callithrix jacchus	ENSCJAG00000008703	1 retrocopy	retro_cjac_724,
Equus caballus	ENSECAG00000016982	1 retrocopy	retro_ecab_148 ,
Microcebus murinus	ENSMICG00000015263	1 retrocopy	retro_mmur_344,
Macaca mulatta	ENSMMUG00000013973	1 retrocopy	retro_mmul_2500,
Monodelphis domestica	ENSMODG00000002882	1 retrocopy	retro_mdom_1402,
Otolemur garnettii	ENSOGAG00000003974	2 retrocopies	retro_ogar_1041, retro_ogar_1931,
Sorex araneus	ENSSARG00000010539	1 retrocopy	retro_sara_7,