RetrogeneDB ID: retro_cjac_1243

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:5634170..5635871(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021752
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCT3
• Ensembl ID: ENSCJAG00000005776
• Aliases: None
• Description: chaperonin containing TCP1, subunit 3 (gamma) [Source:HGNC Symbol;Acc:1616]

Sequence

>retro_cjac_1243
AGTTCTGGTCCGGAAGGTTCTGTCGGTTCCCCCAGTTCTGGGTACCCGGCTCTGCATCGCGCCGCCATGATGGGCCATCG
TCCCGTGCTCGTGCTCAGCCAGAACACAAAGCGTGAATCCGGAAGAAAAGTTCAATCTGGAAGCATCAATGCTGCCAAGA
CTATTGCAGATATCATCCGAACATGTTTGGGACCCAAGTCCATGATGAAGATGCTATTGGACCCAATGGGAGGCATCGTG
ATGACCAATGATGGCAACGCCATTCTTCGAGAGATTCAGGTCCAGCATCCAGCAGCCAAGTCCATGATTGAAATTAGCCG
GACCCAGGATGAAGAGGTTGGAGATGGGACCACATCAGTAATTATTCTTGCGGGGGAAATGCTGTCTATAGCTGAGCACT
TCCTGGAGCAGCAGATGCACCCAACAGTGGTGATCAGTGCTTACCGCAAGGCATTGGATGATATGATCAGCACCCTAAGG
AAAATCAGTATCCCAGTTGACATCAATAACAGTGATATGATGCTGAACATCATCAATAGCTCCATAACTACCAAAGCCAT
CAGTCGGTGGTCATCTTTGGCTTGCAACATTGCCCTGGATGCTGTCAAGACAGTACAGTTTGAGGAGAATGGTCGGAAAG
AGATTGACATAAAAAAATACGCAAAGGTGGAAAAGATACCTGGGGGCATCATTGAAGACTCCTGTGTCTTGCGTGTAGTC
ATGATTAACAAGGATGTGACCCATCCACGCATGCGACGCTATATCAAGAACCCTCGCATTGTGCTGCTGGATTCTTCTCT
GGAATACAAGAAAGGAGAAAGCCAGACTGACATTGAGATTACACGAGAGGAGGACTTCACACGAATTCTCCAAATGGAAG
AAGAGTATATCCAGCAGCTCTGTGAAGACATTATCCAGCTGAAGCCTGATGTGGTCATCACCGAAAAGGGCATCTCAGAT
TTAGCTCAGCACTACCTCATGCGGGCCAATATCACAGCCATCCGCAGAGTCCGGAAGACAGACAATAATCGCATTGCTAG
AGCCTGTGGGGCCCGGATAGTCAGCCGACCAGAGGAACTGAGAGAAGATGATGTTGGAACGGGAGCAGGCCTGTTGGAAA
TCAAGAAAATTGGCGATGAATACTTTACATTCATCACTGAGTGCAAAGACCCCAAGGCCTGCACCATTCTTCTCCGGGGG
GCTAGCAAAGAGATTCTTGCGGAAGTAGAACGCAATCTCCAGGATGCCATGCAAGTGTGCCGAAATGTTCTCCTGGACCC
TCAGCTGGTGCCAGGGGGTGGGGCCTCTGAGATGGCTGTGGCCCATGCCTTGACAGAAAAATCCAAGGCCATGACTGGTG
TGGAACAATGGCCATACAGGGCTGTTGCACAGGCCCTAGAGGTCATCCCTCGTACCCTGATCCAGAACTGTGGGGCCAGC
ACCATCCGTCTACTTACCTCCCTTAGGGCCAAGCACACCCAGGAGAACTGTGAGACCTGGGGTGTAAATGGTGAGACGGG
TACTTTGGTGGACATGAAGGAACTGGGCATATGGGAGCCATTGGCTGTGAAGCTGCAGACTTATAAGACAGCAGTGGAGA
CGGCAGTTCTGCTACTGCGAATTGATGACATCGTCTCAGGCCACAAAAAGAAAGGCGATGACCAGAGCCGGCAAGGCGGG
GCTCCTGATGCTGGCCAGGAG

Alignment

ORF - retro_cjac_1243 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.12 %
• Parental protein coverage: 98.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLSPEGSVGSPSSGYPALHRAAMMGHRPVLVLSQNTKRESGRKVQSGNINAAKTIADIIRTCLGPKSMMK
          S..PEGSVGSPSSGYPALHRAAMMGHRPVLVLSQNTKRESGRKVQSG.INAAKTIADIIRTCLGPKSMMK
Retrocopy SSGPEGSVGSPSSGYPALHRAAMMGHRPVLVLSQNTKRESGRKVQSGSINAAKTIADIIRTCLGPKSMMK

Parental  MLLDPMGGIVMTNDGNAILREIQVQHPAAKSMIEISRTQDEEVGDGTTSVIILAGEMLSVAEHFLEQQMH
          MLLDPMGGIVMTNDGNAILREIQVQHPAAKSMIEISRTQDEEVGDGTTSVIILAGEMLS.AEHFLEQQMH
Retrocopy MLLDPMGGIVMTNDGNAILREIQVQHPAAKSMIEISRTQDEEVGDGTTSVIILAGEMLSIAEHFLEQQMH

Parental  PTVVISAYRKALDDMISTLRKISIPVDINNSDMMLNIINSSITTKAISRWSSLACNIALDAVKTVQFEEN
          PTVVISAYRKALDDMISTLRKISIPVDINNSDMMLNIINSSITTKAISRWSSLACNIALDAVKTVQFEEN
Retrocopy PTVVISAYRKALDDMISTLRKISIPVDINNSDMMLNIINSSITTKAISRWSSLACNIALDAVKTVQFEEN

Parental  GRKEIDIKKYAKVEKIPGGIIEDSCVLRGVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEI
          GRKEIDIKKYAKVEKIPGGIIEDSCVLR.VMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEI
Retrocopy GRKEIDIKKYAKVEKIPGGIIEDSCVLRVVMINKDVTHPRMRRYIKNPRIVLLDSSLEYKKGESQTDIEI

Parental  TREEDFTRILQMEEEYIQQLCEDIIQLKPDVVITEKGISDLAQHYLMRANITAIRRVRKTDNNRIARACG
          TREEDFTRILQMEEEYIQQLCEDIIQLKPDVVITEKGISDLAQHYLMRANITAIRRVRKTDNNRIARACG
Retrocopy TREEDFTRILQMEEEYIQQLCEDIIQLKPDVVITEKGISDLAQHYLMRANITAIRRVRKTDNNRIARACG

Parental  ARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITECKDPKACTILLRGASKEILAEVERNLQDAMQVC
          ARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITECKDPKACTILLRGASKEILAEVERNLQDAMQVC
Retrocopy ARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITECKDPKACTILLRGASKEILAEVERNLQDAMQVC

Parental  RNVLLDPQLVPGGGASEMAVAHALTEKSKAMTGVEQWPYRAVAQALEVIPRTLIQNCGASTIRLLTSLRA
          RNVLLDPQLVPGGGASEMAVAHALTEKSKAMTGVEQWPYRAVAQALEVIPRTLIQNCGASTIRLLTSLRA
Retrocopy RNVLLDPQLVPGGGASEMAVAHALTEKSKAMTGVEQWPYRAVAQALEVIPRTLIQNCGASTIRLLTSLRA

Parental  KHTQENCETWGVNGETGTLVDMKELGIWEPLAVKLQTYKTAVETAVLLLRIDDIVSGHKKKGDDQSRQGG
          KHTQENCETWGVNGETGTLVDMKELGIWEPLAVKLQTYKTAVETAVLLLRIDDIVSGHKKKGDDQSRQGG
Retrocopy KHTQENCETWGVNGETGTLVDMKELGIWEPLAVKLQTYKTAVETAVLLLRIDDIVSGHKKKGDDQSRQGG

Parental  APDAGQE
          APDAGQE
Retrocopy APDAGQE

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
SRP051959_colon	1.33 RPM	31.15 RPM
SRP051959_heart	0.95 RPM	28.24 RPM
SRP051959_kidney	1.31 RPM	33.04 RPM
SRP051959_liver	1.36 RPM	43.56 RPM
SRP051959_lung	0.94 RPM	34.99 RPM
SRP051959_lymph_node	2.15 RPM	50.64 RPM
SRP051959_skeletal_muscle	1.33 RPM	38.28 RPM
SRP051959_spleen	1.13 RPM	37.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1243 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1243 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005776	1 retrocopy	retro_cjac_1243 ,
Cavia porcellus	ENSCPOG00000009131	1 retrocopy	retro_cpor_813,
Mus musculus	ENSMUSG00000001416	2 retrocopies	retro_mmus_2352, retro_mmus_824,
Otolemur garnettii	ENSOGAG00000008967	1 retrocopy	retro_ogar_2017,
Rattus norvegicus	ENSRNOG00000019090	2 retrocopies	retro_rnor_1450, retro_rnor_2823,
Ictidomys tridecemlineatus	ENSSTOG00000001798	1 retrocopy	retro_itri_788,