RetrogeneDB ID: retro_cjac_2185

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:126787376..126788431(+)
• 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_2185
AATCTGTGTGATTCTTAGAACGCCTGGCCGCAGGTGAAGGAACTCAAAGAGGCATTAGGTATTCCAGCCGCTGCCTCTTT
CAAACATGTCAGCCCAGCAGGCACTGCTATTGGAATTTCACTCAGTGAAGACGAGGCCAGAGTCTGCATGGTCTTTGATC
TCTATAAAACCCTTACATCCATTTCAACGGCATACGCAAGAGCAAGAGGAGCTGATAGGATGTCTTCATCTGGCGATTTT
GTGGCATTGTCTGACGTTTGTGATGTACCAACTGCAAAAATTATTTCCAGAGATGTCTCTGATGGTATAATTGCCCCAGG
ATATGAAGAAGTCTTGACAATACTTTCCAAAAAGAAAAATGGAAACTACTGTGTTCTTCAGATGGACCAGTTTTACAAAC
CGGATGAAAATGAAGTTCGAACTCTCTTCGGTCTTCATTTAAGCCAGAAGAGAAATAATGGTGTCGTTGACAAGTCATTA
TTTAGCAATGTTGTCACCAAGAATAAAGATCTGCCAGAGTCCGGCCTCTGAGATCTCATCGTAGCCACCATTGCTGTCAA
GTACACTCAGTCCAACTCCGTGTGCTATGCCAAGAACAGGCAGGTTATCGGCATTGGAGCCAGACAGCAGTCTCATATAC
ACTGCACCCACCTTGCAGGAGATAAGGCAAACTACTGGTGGCTTAGACACCATTCACAAGTGCTCTTGTTGAAGTTTAAA
AAGGGAGGGAAGAGAGCAGAAATCTTCAGTGCCATCGATTAATACGTGTCTGGAACTATTGGCAAGGATGAAGATTTGAT
AAAGTGGAAGGCCCTGTTTGAGGAAGTCCCTGAATTACTCACTGAGGCAGAGAAGAAGGAATGAGTTGACAAACTGAGTG
AGGTTTCTGTCAGCTCTGATGCCTTCTTCCCTTTCAGAGATAAAGTAGACAGAGCTAAAAGGAGTGGTGTGGCATACATT
GTGGCTCCCTCTGGCTCTGCTCTGGCAAAGTTGTGATTGAGGCCTGCGATGAACTGGGAATCATCCTCGCTCATAGGAAC
CTTCGGCTCTTCCAC

Alignment

ORF - retro_cjac_2185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.83 %
• Parental protein coverage: 59.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLCDALNAWQLVKELKEALGIPAAASFKHVSPAGAAVGIPLSEDEARVCMVFDLYKTLTPISTAYARARG
          NLCD..NAW..VKELKEALGIPAAASFKHVSPAG.A.GI.LSEDEARVCMVFDLYKTLT.ISTAYARARG
Retrocopy NLCDS*NAWPQVKELKEALGIPAAASFKHVSPAGTAIGISLSEDEARVCMVFDLYKTLTSISTAYARARG

Parental  ADRMSSFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALTILSKKKNGNYCVLQMDQSYKPDENEV
          ADRMSS.GDFVALSDVCDVPTAKIISR.VSDGIIAPGYEE..LTILSKKKNGNYCVLQMDQ.YKPDENEV
Retrocopy ADRMSSSGDFVALSDVCDVPTAKIISRDVSDGIIAPGYEE-VLTILSKKKNGNYCVLQMDQFYKPDENEV

Parental  RTLFGLHLSQKRNNGVVDKSLFSNVVTKNKDLPESALRDLIVATIAVKYTQSNSVCYAKNGQVIGIGAGQ
          RTLFGLHLSQKRNNGVVDKSLFSNVVTKNKDLPES.L.DLIVATIAVKYTQSNSVCYAKN.QVIGIGA.Q
Retrocopy RTLFGLHLSQKRNNGVVDKSLFSNVVTKNKDLPESGL*DLIVATIAVKYTQSNSVCYAKNRQVIGIGARQ

Parental  QSRIHCTRLAGDKANYWWLRHHPQVLSMKFKTGVKRAEISNAIDQYVTGTIGEDEDLIKWKALFEEVPEL
          QS.IHCT.LAGDKANYWWLRHH.QVL..KFK.G.KRAEI..AID.YV.GTIG.DEDLIKWKALFEEVPEL
Retrocopy QSHIHCTHLAGDKANYWWLRHHSQVLLLKFKKGGKRAEIFSAID*YVSGTIGKDEDLIKWKALFEEVPEL

Parental  LTEAEKKEWVDKLSEVSVSSDAFFPFRDNVDRAKRSGVAYIAAPSGSA-ADKVVIEACDELGIILAHTNL
          LTEAEKKE.VDKLSEVSVSSDAFFPFRD.VDRAKRSGVAYI.APSGSA...KVVIEACDELGIILAH.NL
Retrocopy LTEAEKKE*VDKLSEVSVSSDAFFPFRDKVDRAKRSGVAYIVAPSGSA<SGKVVIEACDELGIILAHRNL

Parental  RLFH
          RLFH
Retrocopy RLFH

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	0.07 RPM	13.31 RPM
SRP051959_heart	0.00 RPM	14.15 RPM
SRP051959_kidney	0.20 RPM	16.28 RPM
SRP051959_liver	0.00 RPM	18.15 RPM
SRP051959_lung	0.00 RPM	14.30 RPM
SRP051959_lymph_node	0.00 RPM	14.13 RPM
SRP051959_skeletal_muscle	0.02 RPM	15.94 RPM
SRP051959_spleen	0.00 RPM	17.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2185 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2185 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,