RetrogeneDB ID: retro_cjac_568

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82148845..82149867(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000000286
• Aliases: None
• Description: None

Sequence

>retro_cjac_568
ATGGCCTTCGAGGATGTGAACGTGTACTTCTCCCCGGAGGAGTGCAGGCTCCTGGACACAGCACAGAGGGCCCTGTACCA
CCATGTGATGCTGGAAAACTTCACACTTGTGACCTCACTTGGACTCTCCACCTCCCGACCTCTGTGGTCATCCAACTTGA
GTGTGGTGAGGACCCCTGGGTTCCCAGTGTGAAGGACATGACCTTGGCCAGGAACGCCTATGGGAGGCGCAACACTGGTT
CCTGGCGTTTGGAAGAGAATGGAGATGTTTCTGGAGAAGCAGCACGGCCAGGGGCCTTCCCAGATACTCCACCTGTGATG
ACTGCTAGTGTCTTCACTGTTGCCAGTGCCTGCCACAGTACAGAAGGCCTGCAGCAACATCGAGGTGCCTCCCCATCTCG
GGAGAGAAAACCCACTGGGGTGTAGGTGATCTACTGAGAGAGGCTCCTGCTAGGCTCGGGCAGGGACCAAGCCAGCATCA
GCCTGTGACTGACCTCCCTGCTCAGGCCCCCTAAGAGCAGCCGGCCCAGGGAAAAGAGCCTCACAGAGCATCTGGTGCCT
AGGAGGCAGTCCAGGGTGCCCAAGTGTCAGAAGCCATGTGCACCGGAGGCCCCTGGGAGAGCTTTCGGGAACGCCACGGA
CCTGAAGGCCGCCAGTGGTGGAGGGGATCACGGAAAGGGTGTGGCTTAGCAAGAGGCTCAGAGATTCCTCGGTGGCCAGG
AGCCCTCGATCTGGAATGAGCTAGGCTAGGCTCTCCACGCTGGGGAAAAGTCCTTCGGATGCAGGGCGTGCAGCAAAGTG
TTCGTGAAGAGCTCCGACCTCCTCAAGCACCTACGCACTCACACCGGGGAGCGGCCCTACGAGTGCTCCCAGTGCGGCAA
GGCCTTCAGCCAGACGTTGCACCTGACACAGCACCAGCGCATCCACAGCGGCGAGACGCCCTACGCGTGCCCCGCGTGTG
GCAAGGCCCTCAGGCACAGCTCCTCACTGGTGCGGCACCAGCGCATCCACACAGCTGAGAGA

Alignment

ORF - retro_cjac_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.01 %
• Parental protein coverage: 62.57 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAFEDVAVYFSEEEWGLLDTAQRALYRHVMLENFTLVTSLGLSTSRPL-VVIQLERGEDPWVPSVKDMTL
          MAFEDV.VYFS.EE..LLDTAQRALY.HVMLENFTLVTSLGLSTSRPL.VVIQLE.GEDPWVPSVKDMTL
Retrocopy MAFEDVNVYFSPEECRLLDTAQRALYHHVMLENFTLVTSLGLSTSRPL<VVIQLECGEDPWVPSVKDMTL

Parental  ARNAYGRRTTGSWHLEEDGDVSGEAAWPGAFPDTPAVMTASVFPVAGACHSTEGLQQQRGASPSRERKPT
          ARNAYGRR.TGSW.LEE.GDVSGEAA.PGAFPDTP.VMTASVF.VA.ACHSTEGLQQ.RGASPSRERKPT
Retrocopy ARNAYGRRNTGSWRLEENGDVSGEAARPGAFPDTPPVMTASVFTVASACHSTEGLQQHRGASPSRERKPT

Parental  GVSVIYWERLLLGSGRDQASISLRLTSPLRPPKSSRPREKTLKEHLVPGRQSRVPKRQKPCAPEAPGRAF
          GV.VIY.ERLLLGSGRDQASISL.LTS.LRPPKSSRPREK.L.EHLVP.RQSRVPK.QKPCAPEAPGRAF
Retrocopy GV*VIY*ERLLLGSGRDQASISL*LTSLLRPPKSSRPREKSLTEHLVPRRQSRVPKCQKPCAPEAPGRAF

Parental  RNTLDLEAASGQGDHRMGAAWQEPQRLLGGQEPSTWDELGEALHAGEKSFECRACSKVFVKSSDLLKHLR
          .N..DL.AASG.GDH..G.A.QE.QR.LGGQEPS.W.ELG.ALHAGEKSF.CRACSKVFVKSSDLLKHLR
Retrocopy GNATDLKAASGGGDHGKGVA*QEAQRFLGGQEPSIWNELG*ALHAGEKSFGCRACSKVFVKSSDLLKHLR

Parental  THTGERPYECSQCGKAFSQTSHLTQHQRIHSGETPYACPACGKAFRHSSSLVRHQRIHTAEK
          THTGERPYECSQCGKAFSQT.HLTQHQRIHSGETPYACPACGKA.RHSSSLVRHQRIHTAE.
Retrocopy THTGERPYECSQCGKAFSQTLHLTQHQRIHSGETPYACPACGKALRHSSSLVRHQRIHTAER

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	5.06 RPM
SRP051959_heart	0.00 RPM	5.33 RPM
SRP051959_kidney	0.02 RPM	6.90 RPM
SRP051959_liver	0.00 RPM	3.88 RPM
SRP051959_lung	0.00 RPM	6.64 RPM
SRP051959_lymph_node	0.00 RPM	7.40 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.30 RPM
SRP051959_spleen	0.00 RPM	7.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_568 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_568 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000286	1 retrocopy	retro_cjac_568 ,