RetrogeneDB ID: retro_cjac_4221

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:124022848..124023698(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK24
• Ensembl ID: ENSCJAG00000004508
• Aliases: None
• Description: None

Sequence

>retro_cjac_4221
AAATCCACAGATTTTTTTCTGTCTGAGCACGGCGAGGTGAAGCTGGCGGACTTTGGCGTGGCCAGCCAATTGACGGACAC
CCAGATCAAAAGGAACACCTCCATGGGCACCCCGTTCTGGATGGCACCCAAGGTCATCAAACAGTCGGCCTATGAAGACA
TCTGGTCCCTGGGCATACAGCTAATGAACTTGCAAAAGGAGAACCACCTCATTCCGAGCTGCGCCCCATGAAAGTTTTAT
TCCTCATTCCAAAGAACAACCCAGCAGCGTTGGGAGGAAACTGCACAAACCCCTCAAGGAGTTTGTGGAGGCCTATTTAT
TATATAAGGAAACGAGCTTTAAACCCACTGCTAAGGAGTTATTGAAGCACAAGTTTATACTACGAAATGCAACGAAAACT
TCCTACTTGACCGAGCTCATCGACAGGTACAAGAGATGGAAGGCCGAGCAGGGCCACGGAAACTTGAGCTCTGAGGATTC
CCACACGGAAACAGATGGCCAAGCCTTAGGCGGCAGCGATTCTGGTAACTGGGCCTTCACAATCCGAGAAAAAGATCCCA
AGAATCTGGAGAATGGAGCTCTTCAGCCATCGGACTTAGACAGAAATAAGATGAAAGACATCCCAAAGAGGCCTTTCTCT
CTTGTGTTTATTTACAATTATTTCTCCTGTGTTTGCAGAGTTGAAGGAAAAGAGCCAGGCGTGCAGAGGGAACTTGGGAT
CCATTGAAAAGCTGCGAGGGGCCATCTACCTGGCGGAGGAAGCGTGCCCCGGCATCACAGACACCATAGGACCCAGCTAG
TGCAGCGGCTCCAGAAATATTCGCTAAGTGGTGGAGGAACTTCATCCCAC

Alignment

ORF - retro_cjac_4221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.44 %
• Parental protein coverage: 66.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGI-TAIELAR
          K.....LSEHGEVKLADFGVA.QLTDTQIKRNT..GTPFWMAP.VIKQSAY....DIWSLGI.TA.ELA.
Retrocopy KSTDFFLSEHGEVKLADFGVASQLTDTQIKRNTSMGTPFWMAPKVIKQSAYE---DIWSLGI<TANELAK

Parental  GEPPHSELHPMKVLFLIPKNNPPTLEGNYS-KPLKEFVEA-CLNKEPSFRPTARELLKHKFILRNAKKTS
          GEPPHSEL.PMKVLFLIPKNNP..L.GN...KPLKEFVEA..L.KE.SF.PTA.ELLKHKFILRNA.KTS
Retrocopy GEPPHSELRPMKVLFLIPKNNPAALGGNCT<KPLKEFVEAYLLYKETSFKPTAKELLKHKFILRNATKTS

Parental  YLTELIDRYKRWKAEQSHEDSSSEDSDAETDGQA-GGSDSGDWIFTIREKDPKNLE-GALQPSDLDGNKK
          YLTELIDRYKRWKAEQ.H...SSEDS..ETDGQA.GGSDSG.W.FTIREKDPKNLE.GALQPSDLD.NK.
Retrocopy YLTELIDRYKRWKAEQGHGNLSSEDSHTETDGQALGGSDSGNWAFTIREKDPKNLENGALQPSDLDRNKM

Parental  KDIPKRPFS-QCLSTIISPLFAELKEKSQACGGNLGSIEELRGAIYLAEEACPGISDTM-VAQLVQRLQR
          KDIPKRPFS..CL.TIISP.FAELKEKSQAC.GNLGSIE.LRGAIYLAEEACPGI.DT....QLVQRLQ.
Retrocopy KDIPKRPFS>LCLFTIISPVFAELKEKSQACRGNLGSIEKLRGAIYLAEEACPGITDTI<RTQLVQRLQK

Parental  YSLSGGGTSSH
          YSLSGGGTSSH
Retrocopy YSLSGGGTSSH

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	92.54 RPM
SRP051959_heart	0.00 RPM	28.43 RPM
SRP051959_kidney	0.00 RPM	44.37 RPM
SRP051959_liver	0.00 RPM	29.93 RPM
SRP051959_lung	0.00 RPM	37.01 RPM
SRP051959_lymph_node	0.00 RPM	38.79 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.77 RPM
SRP051959_spleen	0.00 RPM	37.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4221 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4221 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4907
Gorilla gorilla	retro_ggor_3065
Macaca mulatta	retro_mmul_2640

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004508	1 retrocopy	retro_cjac_4221 ,
Callithrix jacchus	ENSCJAG00000006066	1 retrocopy	retro_cjac_1090,
Cavia porcellus	ENSCPOG00000006610	1 retrocopy	retro_cpor_490,
Homo sapiens	ENSG00000102572	1 retrocopy	retro_hsap_4907,
Gorilla gorilla	ENSGGOG00000001983	1 retrocopy	retro_ggor_3065,
Macaca mulatta	ENSMMUG00000009173	1 retrocopy	retro_mmul_2640,
Nomascus leucogenys	ENSNLEG00000007854	1 retrocopy	retro_nleu_2352,