RetrogeneDB ID: retro_cjac_1906

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:45314634..45315335(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021264
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015051
• Aliases: None
• Description: None

Sequence

>retro_cjac_1906
GAGAAACAGCACAGCATTCTGGGTTCTGGATTTAAAGCTGAGCGCTTAAGAGTCAATTTGAGATTAGTCATAAATCACCT
TAAACTTTTGGAGAAAAAAAAAACGGAACTGGCGCAGAAAGCAAGGAAGGAGATTGCCAACTATCTGGCTGCTGGGAAAG
ATGAACGAGCTTGGATCCGTATGGAGCACATTATCCGGGAAGACCACCTTGTGGAGGCCATGGAGATCCTGGAGCTGTAC
TGTGATCTGCTGCTGGCTCGGTTTGGCCTTATCCAGTCTATGAAGGAGCTAGATTCTGGTCTGGCTGAATCTGTGTCTAC
ACTGATCTGGGCTGCTCCTCGACTCCAGTCAGGGTGGCTGAGTTGAAAATAGCTGCTGATCAGCTCTGTGCCAAGTATAG
CAAGGAATATGGCACGTTATGTAGGACCAACCAGATTGGAACTGTGAATGACAGGCTAATGCACAAACTGAGTGTGGAAG
CCCCACCTAAAATCCTGGTGGAGAGATACCTGATTGAAATTGTGAAGAATTACAATGTACCCTATGAGCCTGACTCTGTG
GTCATGGCAGAAGCCCCACCTGGGGTAGAGACAGATCTTATTGATGTTGGGTTCACAATTGATGTGAAGAAAGGAGGCCC
TGGAAGAGGAGGAGGAGGGGGTGGTGGCTTCACAGCACCAGTTGGTGGACCTGATGGAACA

Alignment

ORF - retro_cjac_1906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.04 %
• Parental protein coverage: 61.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKQYSMLGSGFKAERLRVNLRLVINRLKLLEKKKTELAQKARKEIADYLAAGKDERARIRVEHIIREDYL
          EKQ.S.LGSGFKAERLRVNLRLVIN.LKLLEKKKTELAQKARKEIA.YLAAGKDERA.IR.EHIIRED.L
Retrocopy EKQHSILGSGFKAERLRVNLRLVINHLKLLEKKKTELAQKARKEIANYLAAGKDERAWIRMEHIIREDHL

Parental  VEAMEILELYCDLLLARFGLIQSMKELDSGLAESVSTLIWAAPRLQS-EVAELKIVADQLCAKYSKEYGK
          VEAMEILELYCDLLLARFGLIQSMKELDSGLAESVSTLIWAAPRLQS..VAELKI.ADQLCAKYSKEYG.
Retrocopy VEAMEILELYCDLLLARFGLIQSMKELDSGLAESVSTLIWAAPRLQS<RVAELKIAADQLCAKYSKEYGT

Parental  LCRTNQIGTVNDRLMHKLSVEAPPKILVERYLIEIAKNYNVPYEPDSVVMAEAPPGVETDLIDVGFTDDV
          LCRTNQIGTVNDRLMHKLSVEAPPKILVERYLIEI.KNYNVPYEPDSVVMAEAPPGVETDLIDVGFT.DV
Retrocopy LCRTNQIGTVNDRLMHKLSVEAPPKILVERYLIEIVKNYNVPYEPDSVVMAEAPPGVETDLIDVGFTIDV

Parental  KKGGPGRGGGGGGGFIAPVGGPDGT
          KKGGPGRGGGGGGGF.APVGGPDGT
Retrocopy KKGGPGRGGGGGGGFTAPVGGPDGT

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	0.04 RPM	34.43 RPM
SRP051959_heart	0.04 RPM	28.85 RPM
SRP051959_kidney	0.13 RPM	42.93 RPM
SRP051959_liver	0.02 RPM	18.76 RPM
SRP051959_lung	0.03 RPM	40.95 RPM
SRP051959_lymph_node	0.05 RPM	38.83 RPM
SRP051959_skeletal_muscle	0.11 RPM	56.36 RPM
SRP051959_spleen	0.04 RPM	34.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1906 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1906 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015051	1 retrocopy	retro_cjac_1906 ,
Dipodomys ordii	ENSDORG00000002409	1 retrocopy	retro_dord_398,
Gorilla gorilla	ENSGGOG00000001863	1 retrocopy	retro_ggor_1446,
Mustela putorius furo	ENSMPUG00000007857	1 retrocopy	retro_mputfur_415,
Pongo abelii	ENSPPYG00000007522	1 retrocopy	retro_pabe_1695,
Sus scrofa	ENSSSCG00000002743	1 retrocopy	retro_sscr_349,