RetrogeneDB ID: retro_cjac_1837

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:125735220..125736183(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012500
• Aliases: None
• Description: None

Sequence

>retro_cjac_1837
CAGATCTATTCCAAGCCTCAACACCACCCAGAGATGAGATTCTTCCAGTGGTTCCACAAATGGAAGCTGCATAGTGACCA
AGAGTACGAGGTCACCTGGTATGTATCCTGGAGCCCCTGCCCAGTGTGTGCCAGGAATGTGGCCAAGTTCCTGGCTGAGG
ACGCGAAGGTCACCCTGACCATCTTCGTGGCCCACCTCTACTACTTCTGGGACCCACATTCCTGGAGGAGCTTCACAGAC
TGTCAGAAAAGAGACAGTCCACATGCCACCATGAAGACTATGAGTTATGGTGACTTTCAGCACTGTTGGGGCAAGTTCGT
GTACAACCAAAAATTGTACAAGCCTTGGAATAAGCTGCCTAAACATTATACATTACTGTGCATCCCGCTGGGGAAGGTTC
TCAGACACCTGATGGATCCAGGCACATTCACTTGCAACTTTACCAATGACCCTTTGGTCCTTGGACGGCACCAAACCTAC
CTGTGTTATTAGGTGGAGCACCTGCACAATGGCACCTGCATCTCGCTGGAGCAGCACAGGGACTTCATACTCAACGAGGC
TTCAAATAATCCTGGTTTCCCTGTAGGCTGCCATGCAGAGCTGTGCCTCCTGGACCTGATTTCCTTTTGGAAGCTGAAAC
AGGCCCAGTGCTACAGGGTCACCTGCTTCATCTCTTGGAGCCCCTGCTTCAGCTGTGCCAAGAAGGTGGCTGAATTTCCT
CAAGAGAACCCATATGCAAGCCTGTGCATCTTCGCTGCCCGCATCTATGATTATCAGCAAGGATATAAAAAGGGCCTGTG
CAGGCTGGACAGAGCTGGGGCCCCAATTTCCAGGATGAAATACAGTGAGTTTAGGCACTGCTGGGACAACTTTCTGGATC
ACCAGGGACACCCCTTCCAGCCCTGGGAGGGCCTAGATGAGCACAGCCAAGCCCTGAGTGGGAGGTTGCAGGCCATTCTC
CAG

Alignment

ORF - retro_cjac_1837 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.54 %
• Parental protein coverage: 98.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVYLKPQHHAEMRFLHWFRKWKLHSDQEYEVTWFVSWSPCPVCARNVAEFLTEDGKVTLTIFVARLYYFW
          Q.Y.KPQHH.EMRF..WF.KWKLHSDQEYEVTW.VSWSPCPVCARNVA.FL.ED.KVTLTIFVA.L.Y..
Retrocopy QIYSKPQHHPEMRFFQWFHKWKLHSDQEYEVTWYVSWSPCPVCARNVAKFLAEDAKVTLTIFVAHL-YYF

Parental  IPRYREELRRLCQRRDSPHATMKIMSYGEFQHCWDKFVDNKTETFAPWNELPKNYTLLRITLGEVLRDLM
          ...........CQ.RDSPHATMK.MSYG.FQHCW.KFV.N......PWN.LPK.YTLL.I.LG.VLR.LM
Retrocopy WDPHSWRSFTDCQKRDSPHATMKTMSYGDFQHCWGKFVYNQ-KLYKPWNKLPKHYTLLCIPLGKVLRHLM

Parental  DPDTFTYNFTNDPSVLGRHQTYLCYEVEHLHSGTWVPLHQHRGFILNEASNSLSFPEGRHAELCLLDLIL
          DP.TFT.NFTNDP.VLGRHQTYLCY.VEHLH.GT...L.QHR.FILNEASN...FP.G.HAELCLLDLI.
Retrocopy DPGTFTCNFTNDPLVLGRHQTYLCY*VEHLHNGTCISLEQHRDFILNEASNNPGFPVGCHAELCLLDLIS

Parental  FWKLDPAQRYRVTCFISWSPCFCCAQEVAEFLQENPHVNLRIFAARIYDYRPGYEEGLCRLSWAGAPISM
          FWKL..AQ.YRVTCFISWSPCF.CA..VAEF.QENP...L.IFAARIYDY..GY..GLCRL..AGAPIS.
Retrocopy FWKLKQAQCYRVTCFISWSPCFSCAKKVAEFPQENPYASLCIFAARIYDYQQGYKKGLCRLDRAGAPISR

Parental  MKYSEFSHCWDTFVDHQGHPFQPWEGLDEHSQALSGRLQAILQ
          MKYSEF.HCWD.F.DHQGHPFQPWEGLDEHSQALSGRLQAILQ
Retrocopy MKYSEFRHCWDNFLDHQGHPFQPWEGLDEHSQALSGRLQAILQ

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	1.69 RPM
SRP051959_heart	0.02 RPM	0.26 RPM
SRP051959_kidney	0.02 RPM	0.62 RPM
SRP051959_liver	0.00 RPM	0.45 RPM
SRP051959_lung	0.07 RPM	2.34 RPM
SRP051959_lymph_node	0.09 RPM	5.11 RPM
SRP051959_skeletal_muscle	0.07 RPM	0.20 RPM
SRP051959_spleen	0.02 RPM	2.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1837 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1837 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1837 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	ENSCJAG00000012500	1 retrocopy	retro_cjac_1837 ,