RetrogeneDB ID: retro_cjac_93

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:88100048..88101068(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022550
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005695
• Aliases: None
• Description: None

Sequence

>retro_cjac_93
ATGGCGGCCGCGGTGGCGACGGCACCCGGGACGTTGGGATCCCTGCATGCTGGCGGCGTCCGCCTAGTAGCTGCTTGTAA
TGCGCGGCTCTGCCAGGGGTTGAGGTTTCCCGGCTCGTTGGCAGGCCGGCGGGTGGGCCAGGCGATCTGGGCCCAGAGCT
GGGTGCCTGTGGCCGGGGGTCCCGCACCAAGAAGGGGCTACAGCTCTGAGGTGAAGACGGAGGACGAACTACGGGTGCGG
CACCTGGAGGACGAGAACCGAGGAATTGTGGTGCTTGGAATAAACAGAGCTTATGGCAAAAATTCACTCAGTAAAAATCT
TATAAAAATGCTATCAAAAGCTGTGGATGCTTTGAAATCTGATAAGAAAGTACGGACCATAATAATCAGGAGTGAAGTCC
CAGGGATATTTCGTGCTGGTGCTGACCTTAAGGAAAGAGCCAAAATGAGTTCCAGTGAAGTTGGTCCTTTTGTCTCCAAA
ATAAGAGCAGTGATTAATGATATTGCTAATCTTCCAGTGCCAATGATTGCAGCAATAGATGGACTCGCTTTAGGTGGTGG
TCTTGAACTGGCTTTAGCTTGTGATATACGAGTAGCAGCTTCCTCTGCAAAAATGGGCCTGGTTGAAACAAAATTGGCAA
TTATTCCTGGTGGAGTGGGGACACAGCGATTGCCACGTGCCATTGGAATGTCCCTGGCCAAGGAGCTCATATTCTCTGCG
CGAGTCCTTGATGGCCAGGAAGCCAAAGCAGTGGGCTTAATCAGCCATGTTCTGGAACAGAACCAGGAGGGAGATGCTGC
CTACAGAAAGGCCCTGGACCTGGCAAGAGAGTTTTTACCTCAGGGACCTGTTGCAGTGAGAGTGGCAAAATTAGCAATTA
ATCAAGGCATGGAGGTCGATTTAGTAACAGGGTTAGCCATGGAAGAAGCTTGTTATGCTCAGACCATTCCAACGAAAGAC
AGACTTGAAGGTCTTCTTGCTTTTAAAGAGAAAAGGCCCCCTCGCTATAAAGGAGAATAA

Alignment

ORF - retro_cjac_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVAMAPGTLGSLHAGGVRLVAACNAWLCQGLRLPGSLAGRRVGPAIWAQSWVPVAGGPAPRRGYSSE
          MAAAVA.APGTLGSLHAGGVRLVAACNA.LCQGLR.PGSLAGRRVG.AIWAQSWVPVAGGPAPRRGYSSE
Retrocopy MAAAVATAPGTLGSLHAGGVRLVAACNARLCQGLRFPGSLAGRRVGQAIWAQSWVPVAGGPAPRRGYSSE

Parental  VKTEDELRVRHLEDENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAG
          VKTEDELRVRHLEDENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGIF.AG
Retrocopy VKTEDELRVRHLEDENRGIVVLGINRAYGKNSLSKNLIKMLSKAVDALKSDKKVRTIIIRSEVPGIFRAG

Parental  ADLKERAKMSSSEVGPFVSKIRAVINDIANLPVPTIAAIDGLALGGGLELALACDIRVAASSAKMGLVET
          ADLKERAKMSSSEVGPFVSKIRAVINDIANLPVP.IAAIDGLALGGGLELALACDIRVAASSAKMGLVET
Retrocopy ADLKERAKMSSSEVGPFVSKIRAVINDIANLPVPMIAAIDGLALGGGLELALACDIRVAASSAKMGLVET

Parental  KLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQNQEGDAAYRKALDLAREFLP
          KLAIIPGG.GTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQNQEGDAAYRKALDLAREFLP
Retrocopy KLAIIPGGVGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVLEQNQEGDAAYRKALDLAREFLP

Parental  QGPVAVRVAKLAINQGMEVDLVTGLAIEEACYAQTIPTKDRLEGLLAFKEKRPPRYKGE
          QGPVAVRVAKLAINQGMEVDLVTGLA.EEACYAQTIPTKDRLEGLLAFKEKRPPRYKGE
Retrocopy QGPVAVRVAKLAINQGMEVDLVTGLAMEEACYAQTIPTKDRLEGLLAFKEKRPPRYKGE

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	6.03 RPM
SRP051959_heart	0.00 RPM	10.77 RPM
SRP051959_kidney	0.02 RPM	17.37 RPM
SRP051959_liver	0.02 RPM	18.32 RPM
SRP051959_lung	0.00 RPM	8.10 RPM
SRP051959_lymph_node	0.05 RPM	9.31 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.95 RPM
SRP051959_spleen	0.00 RPM	7.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_93 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_93 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_93 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005695	1 retrocopy	retro_cjac_93 ,
Callithrix jacchus	ENSCJAG00000021374	5 retrocopies	retro_cjac_2675, retro_cjac_3927, retro_cjac_4003, retro_cjac_4228, retro_cjac_4229,
Cavia porcellus	ENSCPOG00000001066	1 retrocopy	retro_cpor_503,
Oreochromis niloticus	ENSONIG00000011227	1 retrocopy	retro_onil_68,
Pan troglodytes	ENSPTRG00000021099	1 retrocopy	retro_ptro_1612,