RetrogeneDB ID: retro_cjac_1210

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:54699167..54700344(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033118
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PADI6
• Ensembl ID: ENSCJAG00000007733
• Aliases: None
• Description: None

Sequence

>retro_cjac_1210
GTGGCTCCCTGCATCTTCATCCCTGCACCCAGTGCCTCTGGAGGTTTATCTGTGCAGGGAGCTGCAGCTGCAGGGTTTTG
TGGACACAGTGATGGAGCTGAGTAAGAAGAGCAACAGCCAGGTGGCCTCTGTCTACGAGGACCCCAGCCGCCTGGGCAGG
TGGCTCCAGGATGAGATGGCCTTCTGCTACACCCAGGCGCCCCACAAGACCACATCCTTGATCCTCGACACGCCTCGAGC
CCCCAATCTTGATGAGTTCCCCATGAAATACTCACTGAGCCCCGGTATTGGCTACATGATCCACGACACTGAAGACCATA
AAGTGGCCAGCATGGATTCCATCGGGAACGTGATGGTGTCCCCACCTGTCAAGGTCCAAGGGAAAGAATACCCCCTGGGC
AGAGTCCTCATTGGCAGCAGCTTTTACCCCAGCATGGAGGGCCGGGCCATGAGTAAGACCCTCCGAGACTTCCTCTATGC
CCAGCAGGTCCAAGCACCGGTGGAGCTCTACTCAGATTGGCTGATGACTGGCCACGTGGATGAGTTCATGTGTTTCATCC
CCACAGATGATAAGAGTGAGGGCAAAAAGGGCTTCCAGCTGCTCCTGGCCAGCCCCGGCGCCTGCTACAAACTCTTCCAA
GAGAAACGGAAGGAAGGCTATGGTGATGCTTTTCTGTTTGACGGAGTTAGAGCAGATCAACTCCTGTCTAACAGAAGAGA
AGCCAAAACCATTGACCAACTTCTGGCTGATGAAAGCCTGAGGAAGCAGAATGAATATGTGGAGAAGTGCATTCACCTGA
ACCATGACATCCTGAAGACAGAGCTGGGCCTGGTGGAACAGGACATCATCGAGATTCCCCAGCTGTTCTGCTTAGAGAAG
CTGACTAATGTGCCCTCTGATCAGCAGCCTAAGACGAGCTTCGCGAGGCCATACTTCCCTAACCTGCTGCGGATGATTGT
GATGGGCAAGAACCTGGGGATCCCCAAGCCTTTTGGGCCCCAAATCAGGGGCACTTGCTGCCTGGAAGAAAAGATACGCT
GCCTGCTGGAGCCCCTGGGCTTCAAGTGCACCTTCGCCAGTGACTTCGACTGCTACCTGGCGGATGTGGGAGATATCTGT
GCCTGTGCCACCGTCCGCCGAGTGCCCTTTGCCTTCAAATGGTGGAAGATGGTACCT

Alignment

ORF - retro_cjac_1210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.23 %
• Parental protein coverage: 56.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAPCIFIP-CTQ-VPLEVYLCRELQLQGFVDTVMELSKKSNSQVASVYEDPSRLGRWLQDEMAFCYTQAP
          VAPCIFIP.CTQ.VPLEVYLCRELQLQGFVDTVMELSKKSNSQVASVYEDPSRLGRWLQDEMAFCYTQAP
Retrocopy VAPCIFIP<CTQ<VPLEVYLCRELQLQGFVDTVMELSKKSNSQVASVYEDPSRLGRWLQDEMAFCYTQAP

Parental  HKTTSLILDTPRAPNLDEFPMKYSLSPGIGYMIHDTEDHKVASMDSIGNVMVSPPVKVQGKEYPLGRVLI
          HKTTSLILDTPRAPNLDEFPMKYSLSPGIGYMIHDTEDHKVASMDSIGNVMVSPPVKVQGKEYPLGRVLI
Retrocopy HKTTSLILDTPRAPNLDEFPMKYSLSPGIGYMIHDTEDHKVASMDSIGNVMVSPPVKVQGKEYPLGRVLI

Parental  GSSFYPSMEGRAMSKTLRDFLYAQQVQAPVELYSDWLMTGHVDEFMCFIPTDDKSEGKKGFQLLLASPGA
          GSSFYPSMEGRAMSKTLRDFLYAQQVQAPVELYSDWLMTGHVDEFMCFIPTDDKSEGKKGFQLLLASPGA
Retrocopy GSSFYPSMEGRAMSKTLRDFLYAQQVQAPVELYSDWLMTGHVDEFMCFIPTDDKSEGKKGFQLLLASPGA

Parental  CYKLFQEKRKEGYGDAFLFDGVRADQLLSNSKREAKTIDQLLADESLRKQNEYVEKCIHLNHDILKTELG
          CYKLFQEKRKEGYGDAFLFDGVRADQLLSN..REAKTIDQLLADESLRKQNEYVEKCIHLNHDILKTELG
Retrocopy CYKLFQEKRKEGYGDAFLFDGVRADQLLSN-RREAKTIDQLLADESLRKQNEYVEKCIHLNHDILKTELG

Parental  LVEQDIIEIPQLFCLEKLTNVPSDQQPKRSFARPYFPNLLRMIVMGKNLGIPKPFGPQIKGTCCLEEKIR
          LVEQDIIEIPQLFCLEKLTNVPSDQQPK.SFARPYFPNLLRMIVMGKNLGIPKPFGPQI.GTCCLEEKIR
Retrocopy LVEQDIIEIPQLFCLEKLTNVPSDQQPKTSFARPYFPNLLRMIVMGKNLGIPKPFGPQIRGTCCLEEKIR

Parental  CLLEPLGFKCTFVSDFDCYLADVGDICACATVRRVPFAFKWWKMVP
          CLLEPLGFKCTF.SDFDCYLADVGDICACATVRRVPFAFKWWKMVP
Retrocopy CLLEPLGFKCTFASDFDCYLADVGDICACATVRRVPFAFKWWKMVP

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	0.04 RPM
SRP051959_heart	0.00 RPM	0.04 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.04 RPM
SRP051959_lung	0.00 RPM	0.15 RPM
SRP051959_lymph_node	0.00 RPM	0.62 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.00 RPM	0.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1210 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1210 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007733	2 retrocopies	retro_cjac_1086, retro_cjac_1210 ,
Sus scrofa	ENSSSCG00000003484	1 retrocopy	retro_sscr_1118,