RetrogeneDB ID: retro_cjac_285

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286243.1:66195..67377(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011987
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000000511
• Aliases: None
• Description: None

Sequence

>retro_cjac_285
TCCATTTTTGGGGGCACGGATATGAAGAAGGCCATTGCCTGCCTGCTCTTTGGGGGATCCCGAAAGAGGCTCCCTGATGG
ACTTACTCGCCGAGGAGACATCAACCTGCTGATGCTAGGGGACCCTGGGACAGCCAAGTCCCAGCTTCTGAAGTTTGTGG
AGAAGTGTTCTCCCATTGGGGTTTACACGTCTGGGAAAGGGAGCAGTGCAGCCGGACTGACAGCCTCGGTGATGAGGGAC
CCTTCGTCCCGGAATTTCATCATGGAAGGTGGAGCCATGGTCCTGGCTGATGGTGGGGTCGTCTGTATTGATGAGTTTGA
CAAGATGCGAGAAGACGACCGTGTGGCAATCCATGAAGCCATGGAGCAGCAGACCATCTCTATTGCCAAGGCTGGGATCA
CCACCACCCTGAACTCTCGCTGCTCCGTCCTGGCTGCTGCCAACTCAGTGTTTGGCCGCTGGGATGAGACGAAGGGGGAG
GACAACATTGATTTCATGCCTACCATCTTGTCGCGCTTCGATATGATCTTCATTGTCAAGGATGAGCACAATGAGGAGAG
GGATGTGATGCTGGCCAAGCATGTCATTACTCTGCACGTAAGTGCACTGACACAGACACAGGCCGTGGAGGGCGAGATCG
ACCTGGCCAAGCTGAAGAAGTTTATTGCCTACTGCCGAGCGAGGTGCGGCCCCCGGCTGTCAGCAGAGGCCGCAGAGAAG
CTGAAGAACCGCTACATCATCATGCGGAGCGGGGCCCGTCAGCACGAGAGGGACAGTGACCGCCGCTCCAGCATCCCCAT
CACTGTGCGGCAGCTGGAGGCCATTGTGCGAATCGCTGAAGCCCTCAGCAAGATGAAGCTGCAGCCCTTCGCCACAGAGG
CAGATGTGGAGGAGGCCCTGCGGCTCTTCCAAGTGTCCACGTTGGATGCTGCCTTGTCCGGTACCCTGTCAGGGGTGGAG
GGCTTCACCAGCCAGGAGGACCAGGAGATGCTGAGCCGCATCGAGAAGCAGCTCAAGCGCCGCTTTGCCATTGGCTCCCA
GGTGTCTGAGCACAGCATTATCAAGGACTTCACCAAGCAGAAATACCCGGAACATGCCATCCTCAAGGTGCTGCAGCTCA
TGCTGCGGCGGGGCGAGATCCAGCATCGCATGCAGCGCAAAGTTCTCTACCGCCTCAAGTGA

Alignment

ORF - retro_cjac_285 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.67 %
• Parental protein coverage: 53.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLVGGWTGDLAVLTLPISPSFPRLPDGLTRRGDINLLMLGDPGTAKSQLLKFVEKCSPIGVYTSGKGSSA
          ...GG.....A...L....S..RLPDGLTRRGDINLLMLGDPGTAKSQLLKFVEKCSPIGVYTSGKGSSA
Retrocopy SIFGGTDMKKAIACLLFGGSRKRLPDGLTRRGDINLLMLGDPGTAKSQLLKFVEKCSPIGVYTSGKGSSA

Parental  AGLTASVMRDPSSRNFIMEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSR
          AGLTASVMRDPSSRNFIMEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSR
Retrocopy AGLTASVMRDPSSRNFIMEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSR

Parental  CSVLAAANSVFGRWDETKGEDNIDFMPTILSRFDMIFIVKDEHNEERDVMLAKHVITLHVSALTQTQAVE
          CSVLAAANSVFGRWDETKGEDNIDFMPTILSRFDMIFIVKDEHNEERDVMLAKHVITLHVSALTQTQAVE
Retrocopy CSVLAAANSVFGRWDETKGEDNIDFMPTILSRFDMIFIVKDEHNEERDVMLAKHVITLHVSALTQTQAVE

Parental  GEIDLAKLKKFIAYCRARCGPRLSAEAAEKLKNRYIIMRSGARQHERDSDRRSSIPITVRQLEAIVRIAE
          GEIDLAKLKKFIAYCRARCGPRLSAEAAEKLKNRYIIMRSGARQHERDSDRRSSIPITVRQLEAIVRIAE
Retrocopy GEIDLAKLKKFIAYCRARCGPRLSAEAAEKLKNRYIIMRSGARQHERDSDRRSSIPITVRQLEAIVRIAE

Parental  ALSKMKLQPFATEADVEEALRLFQVSTLDAALSGTLSGVEGFTSQEDQEMLSRIEKQLKRRFAIGSQVSE
          ALSKMKLQPFATEADVEEALRLFQVSTLDAALSGTLSGVEGFTSQEDQEMLSRIEKQLKRRFAIGSQVSE
Retrocopy ALSKMKLQPFATEADVEEALRLFQVSTLDAALSGTLSGVEGFTSQEDQEMLSRIEKQLKRRFAIGSQVSE

Parental  HSIIKDFTKQKYPEHAILKVLQLMLRRGEIQHRMQRKVLYRLK
          HSIIKDFTKQKYPEHAILKVLQLMLRRGEIQHRMQRKVLYRLK
Retrocopy HSIIKDFTKQKYPEHAILKVLQLMLRRGEIQHRMQRKVLYRLK

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	4.06 RPM
SRP051959_heart	0.00 RPM	0.25 RPM
SRP051959_kidney	0.00 RPM	0.33 RPM
SRP051959_liver	0.02 RPM	1.21 RPM
SRP051959_lung	0.00 RPM	1.35 RPM
SRP051959_lymph_node	0.00 RPM	2.83 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.24 RPM
SRP051959_spleen	0.02 RPM	4.41 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_285 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_285 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000511	1 retrocopy	retro_cjac_285 ,
Myotis lucifugus	ENSMLUG00000001987	1 retrocopy	retro_mluc_983,