RetrogeneDB ID: retro_cjac_706

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:82506515..82507830(+)
• Located in intron of: None

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_706
GCCTTGTTCAGTGTCTCTGACAAAACCGGCCTTGTGGAATTTGCAAGAAACCTGATCTCTCTCGGTTTGAATCTGGTCGC
TTCCGGAGGGACTGCAAAAGCTCTCAGGGATGCTGGTCTGGCAGTCAGAGATGTCTCTGAGTTGACAGGATTTCCTGAAA
TGTTGGGGGGACGTGTGAAAACTTTGCATCCTGCAGTCCATGCTGGAATCCTGGCTCGCAATATTCCAGAAGATAATGCT
GACATGGCCAGACTTGATTTCGATCTTATAAGAGTTGTTACCTGCAATCTCTATCCCTTTGTGAAGACAGTGGCTTCTCC
AGGTGTAACTGTTGAGGAAGCTGTGGAGCAAATTGACATTGGTGGAGTAACCTTACTGAGAGCTGCAGCCAAAAACCACG
CTCGAGTGACAGTGGTGTGTGAACCTGAGGACTACGTGGCAGTGTCCACAGAGATGCAGAGCTCTGAGAGCAAGGACACC
TCCTTGGAGACTAGACGCCAGTTAGCCTTGAAGGCATTCACTCATACGGCACAATACGATGAAGCAATTTCAGATTATTT
CAGGAAACAGTACAGCAAAGACGTATCTCAGATGCCCTTTCGGTATGGGATGAACCCTCATCAGACCCCTGCCCAGCTGT
ACACACTGAAGCCCAAGCTTCCCATCACAGTTCTAAATGGATTTATAAACCTGTGCGATGCTTTGAATGCCTGGCAGCTG
GTGAAGGAACTCAAAGAGGCGTTAGGTATTCCAGCCGCTGCCTCTTTCAAACATGTCAGCCCAGCAGGTGCCGCTGTTGG
AATTCCACTCAGTGAAGATGAGGCCAGAGTCTGCATGGTTTTTGATCTCTATAAAACCCTTACACCCATTTCAACGGCAT
ACGCAAGAGCAAGAGGGGCTGATAGGATGTCGTCATTTGGCGATTTTGTGGCATTGTCTGACGTTTGTGATGTACCAACT
GCAAAAATTATTTCCAGAGAAGTCTCTGATGGTATAATTGCCCCAGGATATGAAGAAGAAGCCTTGACAATACTTTCCAA
AAAGAAAAATGGAAACCACTGTGTTCTTCAGATGGACCAGTCTTACAAACCAGATGAAAATGAAGTTCGAACGCTCTTTG
GTCTTCATTTAAGCCAGAAGAGAAATAACGGTGTCGTTGACAAGTCATTATTTAGCAATGTTGTCACCAAGAATAAAGAT
CTGCCAGAGTCTGCCCTCCGAGACTCATCGTAGCCACCATTGCTGTCAAGTACACTCAGTCCAACTCCGTGTGTACGCCA
GATGGGCAGGTTATGGCATTGGAGCTGGACAGCAG

Alignment

ORF - retro_cjac_706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.85 %
• Parental protein coverage: 74.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ALFSVSDKTGLVEFARNLISLGLNLVASGGTAKALRDAGLAVRDVSELTGFPEMLGGRVKTLHPAVHAGI
          ALFSVSDKTGLVEFARNLISLGLNLVASGGTAKALRDAGLAVRDVSELTGFPEMLGGRVKTLHPAVHAGI
Retrocopy ALFSVSDKTGLVEFARNLISLGLNLVASGGTAKALRDAGLAVRDVSELTGFPEMLGGRVKTLHPAVHAGI

Parental  LARNIPEDNADMARLDFNLIRVVACNLYPFVKTVASPGVTVEEAVEQIDIGGVTLLRAAAKNHARVTVVC
          LARNIPEDNADMARLDF.LIRVV.CNLYPFVKTVASPGVTVEEAVEQIDIGGVTLLRAAAKNHARVTVVC
Retrocopy LARNIPEDNADMARLDFDLIRVVTCNLYPFVKTVASPGVTVEEAVEQIDIGGVTLLRAAAKNHARVTVVC

Parental  EPEDYVAVSTEMQSSESKDTSLETRRQLALKAFTHTAQYDEAISDYFRKQYSKDVSQMPLRYGMNPHQTP
          EPEDYVAVSTEMQSSESKDTSLETRRQLALKAFTHTAQYDEAISDYFRKQYSKDVSQMP.RYGMNPHQTP
Retrocopy EPEDYVAVSTEMQSSESKDTSLETRRQLALKAFTHTAQYDEAISDYFRKQYSKDVSQMPFRYGMNPHQTP

Parental  AQLYTLKPKLPITVLNGAPGFINLCDALNAWQLVKELKEALGIPAAASFKHVSPAGAAVGIPLSEDEARV
          AQLYTLKPKLPITVLNG...FINLCDALNAWQLVKELKEALGIPAAASFKHVSPAGAAVGIPLSEDEARV
Retrocopy AQLYTLKPKLPITVLNG---FINLCDALNAWQLVKELKEALGIPAAASFKHVSPAGAAVGIPLSEDEARV

Parental  CMVFDLYKTLTPISTAYARARGADRMSSFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALTILSK
          CMVFDLYKTLTPISTAYARARGADRMSSFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALTILSK
Retrocopy CMVFDLYKTLTPISTAYARARGADRMSSFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALTILSK

Parental  KKNGNYCVLQMDQSYKPDENEVRTLFGLHLSQKRNNGVVDKSLFSNVVTKNKDLPESALRD-LIVATIAV
          KKNGN.CVLQMDQSYKPDENEVRTLFGLHLSQKRNNGVVDKSLFSNVVTKNKDLPESALRD.LIVATIAV
Retrocopy KKNGNHCVLQMDQSYKPDENEVRTLFGLHLSQKRNNGVVDKSLFSNVVTKNKDLPESALRD<LIVATIAV

Parental  KYTQSNSVCYAKNGQVI-GIGAGQQ
          KYTQSNSVC....GQV..GIGAGQQ
Retrocopy KYTQSNSVC-TPDGQVM<GIGAGQQ

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	0.11 RPM	13.31 RPM
SRP051959_heart	0.12 RPM	14.15 RPM
SRP051959_kidney	0.09 RPM	16.28 RPM
SRP051959_liver	0.09 RPM	18.15 RPM
SRP051959_lung	0.16 RPM	14.30 RPM
SRP051959_lymph_node	0.16 RPM	14.13 RPM
SRP051959_skeletal_muscle	0.20 RPM	15.94 RPM
SRP051959_spleen	0.15 RPM	17.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_706 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_706 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_706 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,