RetrogeneDB ID: retro_cfam_1969

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:72927605..72928538(-)
• Located in intron of: ENSCAFG00000030258

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT2
• Ensembl ID: ENSCAFG00000000432
• Aliases: None
• Description: chaperonin containing TCP1, subunit 2 (beta) [Source:HGNC Symbol;Acc:1615]

Sequence

>retro_cfam_1969
GGAGTAAATCAACCAAAGCGAATTGAAAATGCTAAAATTCTCATTGCGAATACTGGTATGGATACAGACAAAATAAAGAT
ATTTGGTTCCAGGGTAAGAGTTGATTCTACAGCAAAAGTTGCTGAAATAGAACATGCCGAAAAGGAAAAAATGAAGGAGA
AAGTTGAACATATTCTTAAGCATGGGATAAATTGCTTTATTAATAGGCAGTTAATTTACAATTATCCTGAACAGCTCTTT
GGTGCTGCTGGTGTTATGGCTATCAAACATGCAGATTTGGCAGGTGTGGAATGCCTAGCTGTTGTTACAGGTGGTGAAAT
TGCATCTACCTTTGACCACCCAGAACTAGTGAAGTTTGGAAGTTGCAAGCTTATTGAGGAAGTCATGATTGGAGAAAATA
AACTTATCCACTTTTCTGGGGTAGCCCTTGGTGAAGCTTGTATCATTGTTTTGTGTGGTGCCACTCAACAAATTTCAGAT
GAAGCAGAAAGATCTTTGCATGATGCTCTTTGTGTTCTTGCCCAAACTGTGAGGGATTCTAGAACAGTGTATGGAGGAGG
CTGTTCTGAGATGCTGATGGCTCATGCTGTGACACAGCTTGCCAGTAGAACACCAGGCAAAGAAGCTGTTGCGATGGAGT
CTTATGCTAAAGCGCTGAGAATGTTGCCAACTATCATAGCTGATAACGCAGGCTGTGACAGTGCAGACCGGGTGGCCCAG
CTGGGAGCTGCCCACAGTGAAGGCAACACAACTGCTGGCCTAGATATGAAGGAAGGTACCATCTGAGATATGGCAGTACT
GGGTATAACAGAAAGTTTCCAAGTGAAGCTACAACTTCTTTTGAGTGCAGCTGAAACAACAGAGGTGATTCTGCATGTGG
ACAACATTATCAAAGCAGCACCAAGGAAACGTATCCCTGATCAACACCCCTGT

Alignment

ORF - retro_cfam_1969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.93 %
• Parental protein coverage: 58.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVNQPKRIENAKILIANTGMDTDKIKIFGSRVRVDSTAKVAEIEHAEKEKMKEKVERILKHGINCFINRQ
          GVNQPKRIENAKILIANTGMDTDKIKIFGSRVRVDSTAKVAEIEHAEKEKMKEKVE.ILKHGINCFINRQ
Retrocopy GVNQPKRIENAKILIANTGMDTDKIKIFGSRVRVDSTAKVAEIEHAEKEKMKEKVEHILKHGINCFINRQ

Parental  LIYNYPEQLFGAAGVMAIEHADFAGVERLALVTGGEIASTFDHPELVKLGSCKLIEEVMIGEDKLIHFSG
          LIYNYPEQLFGAAGVMAI.HAD.AGVE.LA.VTGGEIASTFDHPELVK.GSCKLIEEVMIGE.KLIHFSG
Retrocopy LIYNYPEQLFGAAGVMAIKHADLAGVECLAVVTGGEIASTFDHPELVKFGSCKLIEEVMIGENKLIHFSG

Parental  VALGEACTIVLRGATQQILDEAERSLHDALCVLAQTVKDSRTVYGGGCSEMLMAHAVTQLASRTPGKEAV
          VALGEAC.IVL.GATQQI.DEAERSLHDALCVLAQTV.DSRTVYGGGCSEMLMAHAVTQLASRTPGKEAV
Retrocopy VALGEACIIVLCGATQQISDEAERSLHDALCVLAQTVRDSRTVYGGGCSEMLMAHAVTQLASRTPGKEAV

Parental  AMESYAKALRMLPTIIADNAGYDSADLVAQLRAAHSEGNTTAGLDMKEGTIGDMAVLGITESFQVKRQVL
          AMESYAKALRMLPTIIADNAG.DSAD.VAQL.AAHSEGNTTAGLDMKEGTI.DMAVLGITESFQVK.Q.L
Retrocopy AMESYAKALRMLPTIIADNAGCDSADRVAQLGAAHSEGNTTAGLDMKEGTI*DMAVLGITESFQVKLQLL

Parental  LSAAEAAEVILRVDNIIKAAPRKRVPDHHPC
          LSAAE..EVIL.VDNIIKAAPRKR.PD.HPC
Retrocopy LSAAETTEVILHVDNIIKAAPRKRIPDQHPC

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	93.70 RPM
SRP017611_brain	0.00 RPM	74.95 RPM
SRP017611_kidney	0.00 RPM	207.22 RPM
SRP017611_liver	0.00 RPM	62.36 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1969 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1969 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000432	2 retrocopies	retro_cfam_1969 , retro_cfam_2166,
Choloepus hoffmanni	ENSCHOG00000006098	1 retrocopy	retro_chof_272,
Callithrix jacchus	ENSCJAG00000001715	2 retrocopies	retro_cjac_1854, retro_cjac_2579,
Loxodonta africana	ENSLAFG00000006688	1 retrocopy	retro_lafr_351,
Myotis lucifugus	ENSMLUG00000008364	1 retrocopy	retro_mluc_2248,