RetrogeneDB ID: retro_mmus_2352

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:52901801..52902392(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083937
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cct3
• Ensembl ID: ENSMUSG00000001416
• Aliases: Cct3, AL024092, Cctg, Tcp1-rs3, TriC-P5
• Description: chaperonin containing Tcp1, subunit 3 (gamma) [Source:MGI Symbol;Acc:MGI:104708]

Sequence

>retro_mmus_2352
CAGACTGACATTGAGATTACATGAGAGGAGGATTTCACCTGAATCCTGCAAATGGAAGAAGAGTACATCCAGCAGTTGTG
TGAGGATATTATCCAGCTGAAACCTGACGTAGTCATCACAGAAAAGGGCATCTCAGATTTAGCTCAGCACTACCTCATGC
GGGCCAATGTCACAGCCATTTGTAGAGTCTGGAAAACAGACAATAATCACATTGCTAGAGCCTGTAGGGCACGGATAGTC
GACCAATCCAAGGAACTGAGAGAAGATGATGTTGGTACAAGGGCAGGCTTACTGGAAATCAAGAAGATTGGAGATGAGTA
CTTTACCTTCATCACTTACTACAAAGACCCAAAGGCCTGTACCAGTCTTCTTAGAGGAGCCAGCAAAGAGATACTCTCAG
AAGTAGAACGAAACCTCCAGGATGTCATGCAAGTGTGCCACAATGGTCTACTGGACCCTCAGCTGGTGCCTGGTGGTGGA
GCCTCTGAGATGGCTGTGGCCGATGCCTTGAGAGAAAAATCTAAGGCCATGACTGGTGTGGAACAATGGCCATATAGAGC
TGTGGCCCAGGCAGTAGAGGTCATCCCTCAG

Alignment

ORF - retro_mmus_2352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.32 %
• Parental protein coverage: 64.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTDIEITREEDFTRILQMEEEYIHQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAIRRVRKTDNNR
          .TDIEIT.EEDFT.ILQMEEEYI.QLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAI.RV.KTDNN.
Retrocopy QTDIEIT*EEDFT*ILQMEEEYIQQLCEDIIQLKPDVVITEKGISDLAQHYLMRANVTAICRVWKTDNNH

Parental  IARACGARIVSRPEELREDDVGTGAGLLEIKKIGDEYFTFITDCKDPKACTILLRGASKEILSEVERNLQ
          IARAC.ARIV....ELREDDVGT.AGLLEIKKIGDEYFTFIT..KDPKACT.LLRGASKEILSEVERNLQ
Retrocopy IARACRARIVDQSKELREDDVGTRAGLLEIKKIGDEYFTFITYYKDPKACTSLLRGASKEILSEVERNLQ

Parental  DAMQVCRNVLLDPQLVPGGGASEMAVAHALTEKSKAMTGVEQWPYRAVAQALEVIPR
          D.MQVC.N.LLDPQLVPGGGASEMAVA.AL.EKSKAMTGVEQWPYRAVAQA.EVIP.
Retrocopy DVMQVCHNGLLDPQLVPGGGASEMAVADALREKSKAMTGVEQWPYRAVAQAVEVIPQ

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
SRP007412_brain	0.00 RPM	95.67 RPM
SRP007412_cerebellum	0.00 RPM	110.68 RPM
SRP007412_heart	0.00 RPM	101.98 RPM
SRP007412_kidney	0.04 RPM	122.12 RPM
SRP007412_liver	0.00 RPM	93.86 RPM
SRP007412_testis	0.05 RPM	332.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2352 was not detected

EST

No EST(s) were mapped for retro_mmus_2352 retrocopy.

TSS

No TSS is located nearby retro_mmus_2352 retrocopy 5' end.

Lab

retro_mmus_2352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2352 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,