RetrogeneDB ID: retro_cfam_2093

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:70768758..70769597(+)
• Located in intron of: ENSCAFG00000017479

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_2093
ATGCCTGAGAATGTGGCACTGCGGAGCAGGGTGCTTGCCGAGGCTACTGGTGGCTGCAGCAAAACTGCCTATAAGGACCA
TGACAAGCTGACCCAGATCCGCTTCAGCAACATTCCTCGGCCAAAGCTATTGCTGATGCTATTAGAACAAGCCTTGGACT
AAAAGGAATGGATAAAATGATTCAAGATGGAAAAGACGATGTGATCATTAGAAATGATGGTGCCACCATTCTTAAACAAA
TGCAAATGTTACATCCAACAGCCAGAATGGGGGTGGAGCTGTCTAAGGCACAAGATATAGAAGCAGGAGTTGGCATCAAC
CACATCAGTGGTCATCATTCCTGGCTCTCTTAGATTCCTGTACCAAGCTTCTTCAGAAAGGGATTCATCCAACCATCATT
TCTGAGTCATTCCAGAAAGCTTTAGAAAAGGGTATACAAATCTTGACTGACATGTCTCAACCTGTAGAACTCAGTGACAG
AGAAACTTTATTAAATAGTGCTACCACTTCATTGAACTTAAAAGTTGTCTCTCAGTTATTCAAGTCTGATTTCTCCAATG
AGTGTAAATGCAGTGATGAAAGTGATTGACCCAGCCACTGCTACTAGTGTAGAACTTGGAGATATTAAAATAGTTAAGAA
ACTTGGTGGGGCAATTGATGACTGTGAGCTGGTAGAAGGGCTGGTACTTACTCAAAAAGTGGCAAATTCTGGAATACCCA
GAGTTTCAAAGGCTAAGATTGGGCTTACTCAGTTTTGCTTATCTGCTCTCAAAACAGATATGGATAATCAAATAGTAGTT
TCTGACTATGTCCAGATGGACTGAGTACTTTAGGAGGAG

Alignment

ORF - retro_cfam_2093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 51.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPENAAPRSGAPAAAAGGRSKTAYQDRDKPAQIRFSNI-SAAKAVADAIRTSLGPKGMDKMIQDGKGDVT
          MPEN.A.RS...A.A.GG.SKTAY.D.DK..QIRFSNI.S.AKA.ADAIRTSLG.KGMDKMIQDGK.DV.
Retrocopy MPENVALRSRVLAEATGGCSKTAYKDHDKLTQIRFSNI<SSAKAIADAIRTSLGLKGMDKMIQDGKDDVI

Parental  ITNDGATILKQMQVLHPAARMLVELSKAQDIEAGDG-TTSVVIIAG-SLLDSCTKLLQKGIHPTIISESF
          I.NDGATILKQMQ.LHP.ARM.VELSKAQDIEAG.G..T..V.I....LLDSCTKLLQKGIHPTIISESF
Retrocopy IRNDGATILKQMQMLHPTARMGVELSKAQDIEAGVG>STTSVVIIP>ALLDSCTKLLQKGIHPTIISESF

Parental  QKALEKGIEILTDMSRPVELSDRETLLNSATTSLNSKVVSQ-YSSLLSPMSVNAVMKVIDPATATSVDLR
          QKALEKGI.ILTDMS.PVELSDRETLLNSATTSLN.KVVSQ.YSSL.SPMSVNAVMKVIDPATATSV.L.
Retrocopy QKALEKGIQILTDMSQPVELSDRETLLNSATTSLNLKVVSQ>YSSLISPMSVNAVMKVIDPATATSVELG

Parental  DIKIVKKLGGTIDDCELVEGLVLTQKVANSGITRVEKAKIGLIQFCLSAPKTDMDNQIVVSDYVQMDRVL
          DIKIVKKLGG.IDDCELVEGLVLTQKVANSGI.RV.KAKIGL.QFCLSA.KTDMDNQIVVSDYVQMD.VL
Retrocopy DIKIVKKLGGAIDDCELVEGLVLTQKVANSGIPRVSKAKIGLTQFCLSALKTDMDNQIVVSDYVQMD*VL

Parental  REE
          .EE
Retrocopy *EE

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	0.00 RPM	136.90 RPM
SRP017611_liver	0.15 RPM	83.97 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2093 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2093 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,