RetrogeneDB ID: retro_cjac_1372

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:3583781..3584530(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACAT2
• Ensembl ID: ENSCJAG00000011777
• Aliases: None
• Description: None

Sequence

>retro_cjac_1372
TCTGATGGCCTTACAGACGTATTTCACAACTGTCATATGGGGATTACAGCTGAAAATGTAGCCAAAAAGTGGCAAGTGAG
TAGAGAAGATCAGGACAAGGTTGCAGTTCTGTCACAGAACAGGACAGAGAATGCATAGAAAGCTGGCCATTTTGACAAAG
AGATTGTACTAGTTTTTGTGTCATCTAGAAAAGGTCTAATTGAAGTTAAAACAGATGAGTCTCCTCGCCATGGGAGCAAC
ATGGAGGCCATGTCCAAGCTAAAACCTTACTTTCTCACAGATGGAACGGGAACAGTCACCCCAGCTAATGCTTCAGGAAT
GAATGATTGTGCTGCAGCTGTGGTTCTTATGAAGAAGTCAGAAGCTGATAAACGTGGGCTTATACCTTTAGCACAGATAG
TGTCTGGTCGCAAGTGGGTGTGGCGCCTTCCATTATGGGAATAGGACCAATTCCAGCCATAAAGCAAGCTGTTGCAAAAG
CAGGTTGCTCACTGGAGGATGTTGATATATTTGAAATCAATGAAGCCTTTGCAGCTCTCTCTGTTGCAATAGCTAAAGAA
CTTGGACTAAACCCAGAGAAGATCAACATTCAAGGAGGGGCTGTAGCCTTGGGCCACCCTCTTGGAGCATGTGGCTGTCA
AATTCTTGTGACCCTGTTACACACACTGGAGAGAACGGGCGGAAGTCGCGGTGTTGCGGCCCTGTGCATTGGGGGTGGGG
TGGGAATAGCAATGTGTGTTCAGAGAGCA

Alignment

ORF - retro_cjac_1372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.43 %
• Parental protein coverage: 61.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDGLTDAFHNCHMGITAENVAKKWQVSREDQDKVAVLSQNRTENAQKAGHFDKEIVPVFVSSRKGLIEVK
          SDGLTD.FHNCHMGITAENVAKKWQVSREDQDKVAVLSQNRTENA.KAGHFDKEIV.VFVSSRKGLIEVK
Retrocopy SDGLTDVFHNCHMGITAENVAKKWQVSREDQDKVAVLSQNRTENA*KAGHFDKEIVLVFVSSRKGLIEVK

Parental  TDEFPRHGSNIEAMSKLKPYFLTDGTGTVTPANASGMNDGAAAVVLMKKSEADKRGLTPLAQIVS-WSQV
          TDE.PRHGSN.EAMSKLKPYFLTDGTGTVTPANASGMND.AAAVVLMKKSEADKRGL.PLAQIVS.WSQV
Retrocopy TDESPRHGSNMEAMSKLKPYFLTDGTGTVTPANASGMNDCAAAVVLMKKSEADKRGLIPLAQIVS<WSQV

Parental  GVEPSIMGIGPIPAIKQAVAKAGWSLEDVDIFEINEAFAAVSVAIVKELGLNPEKVNIQGGAIALGHPLG
          GV.PSIMGIGPIPAIKQAVAKAG.SLEDVDIFEINEAFAA.SVAI.KELGLNPEK.NIQGGA.ALGHPLG
Retrocopy GVAPSIMGIGPIPAIKQAVAKAGCSLEDVDIFEINEAFAALSVAIAKELGLNPEKINIQGGAVALGHPLG

Parental  ASGCRILVTLLHALERTGGNRGVAALCIGGGMGIAMCVQRA
          A.GC.ILVTLLH.LERTGG.RGVAALCIGGG.GIAMCVQRA
Retrocopy ACGCQILVTLLHTLERTGGSRGVAALCIGGGVGIAMCVQRA

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	0.00 RPM	19.37 RPM
SRP051959_heart	0.00 RPM	3.60 RPM
SRP051959_kidney	0.02 RPM	6.66 RPM
SRP051959_liver	0.00 RPM	122.12 RPM
SRP051959_lung	0.03 RPM	3.94 RPM
SRP051959_lymph_node	0.00 RPM	4.79 RPM
SRP051959_skeletal_muscle	0.04 RPM	3.58 RPM
SRP051959_spleen	0.02 RPM	3.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1372 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1372 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002827	1 retrocopy	retro_btau_560,
Callithrix jacchus	ENSCJAG00000011777	1 retrocopy	retro_cjac_1372 ,
Dasypus novemcinctus	ENSDNOG00000002502	1 retrocopy	retro_dnov_331,
Macaca mulatta	ENSMMUG00000012843	1 retrocopy	retro_mmul_277,
Monodelphis domestica	ENSMODG00000007156	1 retrocopy	retro_mdom_1493,
Rattus norvegicus	ENSRNOG00000019189	1 retrocopy	retro_rnor_1055,
Xenopus tropicalis	ENSXETG00000021174	1 retrocopy	retro_xtro_45,