RetrogeneDB ID: retro_cfam_590

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:10032753..10034313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT4
• Ensembl ID: ENSCAFG00000003083
• Aliases: None
• Description: chaperonin containing TCP1, subunit 4 (delta) [Source:HGNC Symbol;Acc:1617]

Sequence

>retro_cfam_590
GGAAAAGGGAAGCATTTTAAAAAGTGAAGAACAAAGCCAGCGCAGATCTGCTTCAGCAACATCTCTGCGGCCAAAGCTGT
TGCTGATGCTATTAGAACAAGCCTTGGAGCAAAAGGAATGGATAAAATGATTCAAGATGGAAAAGGTGATGTGACCATTA
CAAATGATGGTGCCACCATTCTTAAACAAATGCAAGTGTTACATCCAGCAGCCAGAATGCTGGTGGAGCTGTCTAAGGCA
CAAGATATAGAAGCAGGAGATGGCACCACACCAGTGGTCTTCATTGCTGGCTCTCTCTTAGATTCCTGTACCAAGCTTCT
TCAGAAAGGGATTCATCCAACCATCATTTCTGAGTCATTCCAGAAGGCTTTAGAAAAGGGTATAGAAATCTTGACTGACA
TGTCTCGACCTGTGGAACTCAGTGACAGAGAAACTGTATTAAATAGTGCTACCACTTCCTTGAACTCAAAGGTTGTGTCT
CAGTATTCAAGTCTGCTTTCTCCAATGAGTGTAAATGCAGCGATGAAAGTGACTGACCCAGCCACGGCTACTAGTGTAGA
TCTTAGAGAGATTGAAATAGTTAAGAAACTTGGTGGGACAATTGATGACTGTGAGCTGGTAGAAGGGCTGGTACTTACTC
AGAAGGTGGCAAATTCTGGCATAACCAGAGTTGAAAAGGCTAAGATTGGGCTTATTCAGTTTTGCTTATCTGCTCCCAAA
ATGGATATGGATAATCAAATTGTAGTTTCTGACTATGTCCAGATGGATCGAGTGCTTCGGGAGGAGAGAGCCTATATTCT
CAATTTAGTGAAGCAAATTTAAAAAACAGGATGTAATGTCCTCTTCATACAGAAGTCTATCCTGAGAGATGCTCTTAGTG
ATCTTGCATTACATTTCCTCAACAAGATGAAGATTATGGTGGTTAAGGATATTGAAAGAGAAGACACTGAATTTATTTGT
AAGACAATTGGAACCAAGCCAGTTGCTCATATTGACCAATTCACTGCTGACATGCTGGGATCAGCTGAGTTAGCTGAGGA
GGTCAATTTAAATGGTTCTGGCAAACTGCTTAAGATTACAGGCTGTACAAGCCCCGGAAAAACCGTTACAATTGTTGTTC
GTGGATCTAACAAATTGGTGATTGAAGAATGCTCTATTCATGATGCCCTATGTGTTATTCACTGTTTAGTGAAGAAGAGA
GCTCTTATTGCAGGAGGTGGTGCTCCAGAGATAGAACTGACCCTGCGGTTAACTGAATATTCACAAACATTGAGTGGCAT
GGAATCCTACTGCATTCGTGCTTTTGCAGATGCTATGGAAGCCATTCCATCTACGCTAGCTGAAAATGCTGGCCTGAATC
CCATTTCTACAGTAACAGAACTAGGAAACCGACATGCCCAAGGAGAAAAAACTACTGGCATTAATGTCTGAAAGGGTGGT
ATTTCCAACATTTTGGAGGAACTGGTAGTCCAGCCTTTGTTGGTCTCAGTCAGTGCACTGACTCTAGCAACTGAAACTGT
CCAGAGCATTCTGAAAATTGATGATGTGGTAAACACTCAG

Alignment

ORF - retro_cfam_590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.68 %
• Parental protein coverage: 96.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRSKTAYQDRDKPAQIRFSNISAAKAVADAIRTSLGPKGMDKMIQDGKGDVTITNDGATILKQMQVLHPA
          G..K.....R.KPAQI.FSNISAAKAVADAIRTSLG.KGMDKMIQDGKGDVTITNDGATILKQMQVLHPA
Retrocopy GKGKHFKK*RTKPAQICFSNISAAKAVADAIRTSLGAKGMDKMIQDGKGDVTITNDGATILKQMQVLHPA

Parental  ARMLVELSKAQDIEAGDGTTSVVIIAGSLLDSCTKLLQKGIHPTIISESFQKALEKGIEILTDMSRPVEL
          ARMLVELSKAQDIEAGDGTT.VV.IAGSLLDSCTKLLQKGIHPTIISESFQKALEKGIEILTDMSRPVEL
Retrocopy ARMLVELSKAQDIEAGDGTTPVVFIAGSLLDSCTKLLQKGIHPTIISESFQKALEKGIEILTDMSRPVEL

Parental  SDRETLLNSATTSLNSKVVSQYSSLLSPMSVNAVMKVIDPATATSVDLRDIKIVKKLGGTIDDCELVEGL
          SDRET.LNSATTSLNSKVVSQYSSLLSPMSVNA.MKV.DPATATSVDLR.I.IVKKLGGTIDDCELVEGL
Retrocopy SDRETVLNSATTSLNSKVVSQYSSLLSPMSVNAAMKVTDPATATSVDLREIEIVKKLGGTIDDCELVEGL

Parental  VLTQKVANSGITRVEKAKIGLIQFCLSAPKTDMDNQIVVSDYVQMDRVLREERAYILNLVKQIKKTGCNV
          VLTQKVANSGITRVEKAKIGLIQFCLSAPK.DMDNQIVVSDYVQMDRVLREERAYILNLVKQI.KTGCNV
Retrocopy VLTQKVANSGITRVEKAKIGLIQFCLSAPKMDMDNQIVVSDYVQMDRVLREERAYILNLVKQI*KTGCNV

Parental  LLIQKSILRDALSDLALHFLNKMKIMVVKDIEREDIEFICKTIGTKPVAHIDQFTADMLGSAELAEEVNL
          L.IQKSILRDALSDLALHFLNKMKIMVVKDIERED.EFICKTIGTKPVAHIDQFTADMLGSAELAEEVNL
Retrocopy LFIQKSILRDALSDLALHFLNKMKIMVVKDIEREDTEFICKTIGTKPVAHIDQFTADMLGSAELAEEVNL

Parental  NGSGKLLKITGCTSPGKTVTIVVRGSNKLVIEEAERSIHDALCVIRCLVKKRALIAGGGAPEIELALRLT
          NGSGKLLKITGCTSPGKTVTIVVRGSNKLVIEE...SIHDALCVI.CLVKKRALIAGGGAPEIEL.LRLT
Retrocopy NGSGKLLKITGCTSPGKTVTIVVRGSNKLVIEEC--SIHDALCVIHCLVKKRALIAGGGAPEIELTLRLT

Parental  EYSRTLSGMESYCVRAFADAMEVIPSTLAENAGLNPISTVTELRNRHAQGEKTTGINVRKGGISNILEEL
          EYS.TLSGMESYC.RAFADAME.IPSTLAENAGLNPISTVTEL.NRHAQGEKTTGINV.KGGISNILEEL
Retrocopy EYSQTLSGMESYCIRAFADAMEAIPSTLAENAGLNPISTVTELGNRHAQGEKTTGINV*KGGISNILEEL

Parental  VVQPLLVSVSALTLATETVRSILKIDDVVNTR
          VVQPLLVSVSALTLATETV.SILKIDDVVNT.
Retrocopy VVQPLLVSVSALTLATETVQSILKIDDVVNTQ

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
SRP012049_cerebellum	0.00 RPM	92.94 RPM
SRP017611_brain	0.00 RPM	88.28 RPM
SRP017611_kidney	0.13 RPM	136.90 RPM
SRP017611_liver	0.00 RPM	83.97 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_590 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_590 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_590 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,