RetrogeneDB ID: retro_cjac_1379

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:16368697..16369954(-)
• Located in intron of: ENSCJAG00000013962

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRHL2
• Ensembl ID: ENSCJAG00000015886
• Aliases: None
• Description: None

Sequence

>retro_cjac_1379
ATGTCACATGAGTCGGACAATAATAAAAGACTAGTGGCCTTAGTGCCCATGCCCAGTGACCCTCCATTCAATACCCGAAG
AGCCTATACCAGTGAGGATGAAGCCTGGAAGTCATACTTGGAGAATCCCCTGACGGCGGCCACCAAGGCCTTGATGAGCA
TTAATGGTGATGAGGACAGTGCTGCTGCCCTTGGCCTGCTCCATGACTATTACAAGGTTCCTCGAGACAAGAGGCTGCTG
TCTGTAAGCAAAGCAAGTGACAGCCAAGAAGACCAGGAGAAAAGAAACTGCCTTGGCACGAGTGAAGCCCAGAGTAATTT
GAGTGGAGGGGAAAACAGAGTGCAAGTCCTAAAGACTGTTCCAGTGAACCTTTCTCTAAATCAAGATCACCTGGAGAATT
CCAAGCGGGAGCAGTACAGCATCAGCGTCCCCGAGAGCTCTGCCATCATCCCCGTGTCGGGAATCACTGTGGTGAAAGCT
GAAGATTTCACACCAGTTTTCATGACCCCACCTATGCACTATCCCCGGGGAGGTGGGGAAGAACAACGAGTGGTTATCTT
TGAACAGACTCAGTATGACCTGCCCTCGCTGGCCACCCACAGCGCCTATCTCAAGGATGACCAGCGCAGCACCCCAGACA
GCACGTACAGCAAGAGCTTCAAGGACGCAGCCACAGAGAAATTTCGGAGTGCTTCAGTTGGGGCTGAGGAGTACATGTAT
GATCAGACCTCAAGTGGCAGGTTTCAGTATACCCTGGAAGCCACCAAATCTCTCCGCCAGAAGCAGGGGCAGGGCCCCAT
GACCTACCTCAACAAAGGACAGTTCTATGCCATAACACTCAGCGAGACTGCAGACAACAAATGCTTCCGACATCCCATCA
GCAAAGTCAGGAGCGTGGTGATGGTGGTCTTCAGTGAAGACAAGAACAGAGACGAACAGCTCAAATACTGGAAATACTGG
CACTCTCGGCAGCACACAGCGAAGCAGAGGGTCCTTGACATTGCTGATTACAAGGAGAGCTTTAATACAATTGGAAACAT
TGAAGAGATTGCATATAATGCTGTTTCCTTTACCTGGGACGTGAATGAAGAGGCGAAGATTTTCATCACCATGAATTGCT
TGAGTACAGATTTCTCCTCCCAAAAAGGGGTGAAAGGACTGCCTTTGATGATTCAGATTGACACATACAGTTATAACAAT
CGTAGCAATAAACCCATTCATAGAGCTTATTGCCAGATCAAGGTCTTCTGTGACAAA

Alignment

ORF - retro_cjac_1379 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.37 %
• Parental protein coverage: 67.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSQESDNNKRLVALVPMPSDPPFNTRRAYTSEDEAWKSYLENPLTAATKAMMSINGDEDSAAALGLLYDY
          MS.ESDNNKRLVALVPMPSDPPFNTRRAYTSEDEAWKSYLENPLTAATKA.MSINGDEDSAAALGLL.DY
Retrocopy MSHESDNNKRLVALVPMPSDPPFNTRRAYTSEDEAWKSYLENPLTAATKALMSINGDEDSAAALGLLHDY

Parental  YKVPRDKRLLSVSKASDSQEDPEKRNCLGTSEAQSNLSGGENRVQVLKTVPVNLSLNQDHLENSKREQYS
          YKVPRDKRLLSVSKASDSQED.EKRNCLGTSEAQSNLSGGENRVQVLKTVPVNLSLNQDHLENSKREQYS
Retrocopy YKVPRDKRLLSVSKASDSQEDQEKRNCLGTSEAQSNLSGGENRVQVLKTVPVNLSLNQDHLENSKREQYS

Parental  ISVPESSAIIPVSGITVVKAEDFTPVFMTPPMHYPRGDGEEQRVVIFEQTQYDLPSLAAHSAYLKDDQRS
          ISVPESSAIIPVSGITVVKAEDFTPVFMTPPMHYPRG.GEEQRVVIFEQTQYDLPSLA.HSAYLKDDQRS
Retrocopy ISVPESSAIIPVSGITVVKAEDFTPVFMTPPMHYPRGGGEEQRVVIFEQTQYDLPSLATHSAYLKDDQRS

Parental  TPDSTYSESFKDAATEKFRSASVGAEEYMYDQTSSGTFQYTLEATKSLRQKQGEGPMTYLNKGQFYAITL
          TPDSTYS.SFKDAATEKFRSASVGAEEYMYDQTSSG.FQYTLEATKSLRQKQG.GPMTYLNKGQFYAITL
Retrocopy TPDSTYSKSFKDAATEKFRSASVGAEEYMYDQTSSGRFQYTLEATKSLRQKQGQGPMTYLNKGQFYAITL

Parental  SETGDNKCFRHPISKVRSVVMVVFSEDKNRDEQLKYWKYWHSRQHTAKQRVLDIADYKESFNTIGNIEEI
          SET.DNKCFRHPISKVRSVVMVVFSEDKNRDEQLKYWKYWHSRQHTAKQRVLDIADYKESFNTIGNIEEI
Retrocopy SETADNKCFRHPISKVRSVVMVVFSEDKNRDEQLKYWKYWHSRQHTAKQRVLDIADYKESFNTIGNIEEI

Parental  AYNAVSFTWDVNEEAKIFITVNCLSTDFSSQKGVKGLPLMIQIDTYSYNNRSNKPIHRAYCQIKVFCDK
          AYNAVSFTWDVNEEAKIFIT.NCLSTDFSSQKGVKGLPLMIQIDTYSYNNRSNKPIHRAYCQIKVFCDK
Retrocopy AYNAVSFTWDVNEEAKIFITMNCLSTDFSSQKGVKGLPLMIQIDTYSYNNRSNKPIHRAYCQIKVFCDK

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	2.04 RPM	14.29 RPM
SRP051959_heart	0.84 RPM	0.63 RPM
SRP051959_kidney	2.35 RPM	12.85 RPM
SRP051959_liver	0.50 RPM	0.78 RPM
SRP051959_lung	1.56 RPM	9.40 RPM
SRP051959_lymph_node	0.89 RPM	0.55 RPM
SRP051959_skeletal_muscle	0.81 RPM	0.37 RPM
SRP051959_spleen	0.80 RPM	0.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1379 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1379 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015886	1 retrocopy	retro_cjac_1379 ,