RetrogeneDB ID: retro_cjac_1538

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:21898356..21899634(+)
• Located in intron of: ENSCJAG00000000917

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATIC
• Ensembl ID: ENSCJAG00000011695
• Aliases: None
• Description: None

Sequence

>retro_cjac_1538
GCCTTGTTCAGTGTCTCTGACAAAACCGGCCTTGTGGAATTTGCAAGAAACCTGATCTCTCTCGGTTTGAATCTGGTCGC
TTCCGGAGGGACTGCAAAAGCTCTCAGGGATGCTGGTCTGGCAGTCAGAGATGTCTCTGAGTTGACAGGATTTCCTGAAA
TGTTGGGGGGACGTGTGAAAACTTTGCATCCTGCAGTCCATGCTGGAATCCTGGCTCGCAATATTCCAGAAGATAATGCT
GACATGGCCAGACTTGATTTCAATCTTATAAGAGTTGTTGCCTGCAATCTCTATCCCTTTGTGAAGACAGTGGCTTCTCC
AGGTGTAACTGTTGAGGAAGCTGTGGAGCAAATTGACATTGGTGGAGTAACCTTACTGAGAGCTGCAGCCAAAAACCACG
CTCGAATGACAGTGGTGTGTGAACCTGAGGACTACGTGGCAGTGTCCACAGAGATGCAGAGCTCCGAGAGCAAGGACACC
TCCTTGGAGACTAGACGCCAGTTAGCCTTGAAGGCATTCACTCATACGGCACAATACGATGAAGCAATTTCAGATTATTT
CAGGAAACAGTACAGCAAAGACGTATCTCAGATGCCCTTGCGGTATGGAATGAACCCTCATCAGACCCCTGCCCAGCTGT
ACACACTGAAGCCCAAGCTTCCCATCACAGTTCTAAATGGAGCCCCTGGATTTATAAACCTGTGCGATGCTTTGAATGCC
TGGCAGCTGGTGAAGGAACTCAAAGAGGCGTTAGGTATTCCAGCCGCTGCCTCTTTCAAACATGTCAGCCCAGCAGGTGC
CGCTGTTGGAATTCCACTCAGTGAAGATGAGGCCAGAGTCTGCATGGTTTTTGATCTCTATAAAACCCTTACACCCATTT
CAACGGCATACACAAGAGCAAGAGGGGCTGATAGGATGTAATCATTTGGCGATTTTGTGGCATTGTCTGACGTTTGTGAT
GTACCAACTGCAAAAATTATTTCCAGAGAAGTCTCTGATGGTATAATTGCCCCAGGATATGAAGAAGAAGCCTTGACAAT
ACTTTCCAAAAAGAAAAATGGAAACTACTGTGTTCTTCAGATGGACCAGTCTTACAAACCAGATGAAAATGAAGTTCGAA
CGCTCTTCGGTCTTCATTTAAGCCAGAAGAGAAATAACGGTGTCATTGACAAGTCATTATTTAGCAATGTTGTCACCAAG
AATAAAGATCTGCCAGAGTCTGCCCTCCGAGACCTCATCGTAGCCACCATTGCTGTCAAGTACACTCAGTCCAACTCC

Alignment

ORF - retro_cjac_1538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.06 %
• Parental protein coverage: 72.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALFSVSDKTGLVEFARNLISLGLNLVASGGTAKALRDAGLAVRDVSELTGFPEMLGGRVKTLHPAVHAGI
          ALFSVSDKTGLVEFARNLISLGLNLVASGGTAKALRDAGLAVRDVSELTGFPEMLGGRVKTLHPAVHAGI
Retrocopy ALFSVSDKTGLVEFARNLISLGLNLVASGGTAKALRDAGLAVRDVSELTGFPEMLGGRVKTLHPAVHAGI

Parental  LARNIPEDNADMARLDFNLIRVVACNLYPFVKTVASPGVTVEEAVEQIDIGGVTLLRAAAKNHARVTVVC
          LARNIPEDNADMARLDFNLIRVVACNLYPFVKTVASPGVTVEEAVEQIDIGGVTLLRAAAKNHAR.TVVC
Retrocopy LARNIPEDNADMARLDFNLIRVVACNLYPFVKTVASPGVTVEEAVEQIDIGGVTLLRAAAKNHARMTVVC

Parental  EPEDYVAVSTEMQSSESKDTSLETRRQLALKAFTHTAQYDEAISDYFRKQYSKDVSQMPLRYGMNPHQTP
          EPEDYVAVSTEMQSSESKDTSLETRRQLALKAFTHTAQYDEAISDYFRKQYSKDVSQMPLRYGMNPHQTP
Retrocopy EPEDYVAVSTEMQSSESKDTSLETRRQLALKAFTHTAQYDEAISDYFRKQYSKDVSQMPLRYGMNPHQTP

Parental  AQLYTLKPKLPITVLNGAPGFINLCDALNAWQLVKELKEALGIPAAASFKHVSPAGAAVGIPLSEDEARV
          AQLYTLKPKLPITVLNGAPGFINLCDALNAWQLVKELKEALGIPAAASFKHVSPAGAAVGIPLSEDEARV
Retrocopy AQLYTLKPKLPITVLNGAPGFINLCDALNAWQLVKELKEALGIPAAASFKHVSPAGAAVGIPLSEDEARV

Parental  CMVFDLYKTLTPISTAYARARGADRMSSFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALTILSK
          CMVFDLYKTLTPISTAY.RARGADRM.SFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALTILSK
Retrocopy CMVFDLYKTLTPISTAYTRARGADRM*SFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALTILSK

Parental  KKNGNYCVLQMDQSYKPDENEVRTLFGLHLSQKRNNGVVDKSLFSNVVTKNKDLPESALRDLIVATIAVK
          KKNGNYCVLQMDQSYKPDENEVRTLFGLHLSQKRNNGV.DKSLFSNVVTKNKDLPESALRDLIVATIAVK
Retrocopy KKNGNYCVLQMDQSYKPDENEVRTLFGLHLSQKRNNGVIDKSLFSNVVTKNKDLPESALRDLIVATIAVK

Parental  YTQSNS
          YTQSNS
Retrocopy YTQSNS

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	0.20 RPM	13.31 RPM
SRP051959_heart	0.02 RPM	14.15 RPM
SRP051959_kidney	0.07 RPM	16.28 RPM
SRP051959_liver	0.09 RPM	18.15 RPM
SRP051959_lung	0.03 RPM	14.30 RPM
SRP051959_lymph_node	0.05 RPM	14.13 RPM
SRP051959_skeletal_muscle	0.13 RPM	15.94 RPM
SRP051959_spleen	0.06 RPM	17.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1538 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1538 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011695	4 retrocopies	retro_cjac_1538 , retro_cjac_2185, retro_cjac_3116, retro_cjac_706,
Microcebus murinus	ENSMICG00000014573	1 retrocopy	retro_mmur_1591,
Myotis lucifugus	ENSMLUG00000001830	1 retrocopy	retro_mluc_1370,
Monodelphis domestica	ENSMODG00000015612	1 retrocopy	retro_mdom_1074,
Mustela putorius furo	ENSMPUG00000007676	1 retrocopy	retro_mputfur_1609,
Mus musculus	ENSMUSG00000026192	1 retrocopy	retro_mmus_2729,
Rattus norvegicus	ENSRNOG00000015511	1 retrocopy	retro_rnor_904,