RetrogeneDB ID: retro_cjac_3064

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:37916543..37917548(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NACC2
• Ensembl ID: ENSCJAG00000010665
• Aliases: None
• Description: None

Sequence

>retro_cjac_3064
TTGTCCACCACTGACAGCCCCACCTCTTACCACAACGAGGACGACGAGGAGGACGATGAGGCCTACGACACCATGGTGGA
GGAGCAGTATGGCCAGATGTACATCAAGGCCTCCGGCAGCTACGCAGTGCAAGAGAAGCCTGAGCCAGTACCCCTGGAGA
GCCGCTCCTGTGTCCTCATCCGCCGCGACCTCGTGGCCCTGCCTGCCAGCCTCATCAGCCAGATCGGATACCGCTGCCAC
CCCAAGCTCTACTCGGAGGGGGACCCCAGCGAGAAGCTGGAGCTGGTGGCAGGCTCTGGGGTCTACATCACACGTGGCCA
GCTGATGAACTGCCACCTCTGCGCGGGGGTGAAGCACAAGGTCTTGCTGCGGAAACTTCTGGCCACCTTCTTTGACAAGA
ACACGCTGGCCAACAGCTGCGGGACGGGCATCCGCTCATCCACCAGTGACCCCAGCCGGAAGCCACTGGACAGCCGGGTC
CTGAACGCTGTGAAACTGTACTGTCAGAACTTCGCCCCCAGCTTCAAGGAGAGAGAGATGAATGTGATCGCCGCGGACAT
ATGTACCAACGCCCGCCGCGTTCGCAAGCGCTGGCTGCCCAAGATCAAGTCCATGCTGCCGGAGGGCGTGGAGATGTACC
GCACAGTCATGGGCTCCTCGACCGCCGGCGCGCCCCTTGACCCTGAGTTCCCGCCCGCCACTGTGGCACAGGTGTTCGAG
CAGCGCATCTATGCCGAGCGGCGGAGCGACGCCGCCACCATCGTGGCTCTGAGAACTGATGCCGTGAATGTTGACCTGAG
CGCCGCGGCCAACCCCGCCTTCGACGCCAGTGAGAAGGTGGACGGGGCCGGCTCGGTCATTCAGGAGGTGGCTGCCCCCG
AGCCGCTGCCCACTGGCGGCCAGAGTCCCCCGCAGCCCTTCGAGCAGGGCGGGGGCAGCCCCAGCAAGCCCCAGACGCCG
GCGGCCGTGGCCCGGAGGCCGGAAGGCACCTATACAGGGACTCTG

Alignment

ORF - retro_cjac_3064 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.73 %
• Parental protein coverage: 57.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPTTDSPTSYHNEDDEEDDEAYDTMVEEQYGQMYIKASGSYAVQEKPEPVPLESRSCVLIRRDLVALPAS
          L.TTDSPTSYH..........YDTMVEEQYGQMYIKASGSYAVQEKPEPVPLESRSCVLIRRDLVALPAS
Retrocopy LSTTDSPTSYHXXXXXXXXXXYDTMVEEQYGQMYIKASGSYAVQEKPEPVPLESRSCVLIRRDLVALPAS

Parental  LISQIGYRCHPKLYSEGDPGEKLELVAGSGVYITRGQLMNCHLCAGVKHKVLLRRLLATFFDRNTLANSC
          LISQIGYRCHPKLYSEGDP.EKLELVAGSGVYITRGQLMNCHLCAGVKHKVLLR.LLATFFD.NTLANSC
Retrocopy LISQIGYRCHPKLYSEGDPSEKLELVAGSGVYITRGQLMNCHLCAGVKHKVLLRKLLATFFDKNTLANSC

Parental  GTGIRSSTSDPSRKPLDSRVLNAVKLYCQNFAPSFKESEMNVIAADMCTNARRVRKRWLPKIKSMLPEGV
          GTGIRSSTSDPSRKPLDSRVLNAVKLYCQNFAPSFKE.EMNVIAAD.CTNARRVRKRWLPKIKSMLPEGV
Retrocopy GTGIRSSTSDPSRKPLDSRVLNAVKLYCQNFAPSFKEREMNVIAADICTNARRVRKRWLPKIKSMLPEGV

Parental  EMYRTVMGSSTAGAPLDPEFPPATAAQVFEQRIYAERRSDAATIVALRTDAVNVDLSAAANPAFDTSEEV
          EMYRTVMGSSTAGAPLDPEFPPAT.AQVFEQRIYAERRSDAATIVALRTDAVNVDLSAAANPAFD.SE.V
Retrocopy EMYRTVMGSSTAGAPLDPEFPPATVAQVFEQRIYAERRSDAATIVALRTDAVNVDLSAAANPAFDASEKV

Parental  DGAGSVIQEVAAPEPLPTGGQSPPQPFEQGGGSPSRPQTPAAVARRPEGTYAGTL
          DGAGSVIQEVAAPEPLPTGGQSPPQPFEQGGGSPS.PQTPAAVARRPEGTY.GTL
Retrocopy DGAGSVIQEVAAPEPLPTGGQSPPQPFEQGGGSPSKPQTPAAVARRPEGTYTGTL

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	0.35 RPM	2.86 RPM
SRP051959_heart	0.37 RPM	5.37 RPM
SRP051959_kidney	0.16 RPM	5.44 RPM
SRP051959_liver	0.24 RPM	2.10 RPM
SRP051959_lung	1.09 RPM	4.08 RPM
SRP051959_lymph_node	1.83 RPM	1.12 RPM
SRP051959_skeletal_muscle	0.22 RPM	3.28 RPM
SRP051959_spleen	1.24 RPM	2.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3064 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3064 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3064 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	ENSCJAG00000010665	1 retrocopy	retro_cjac_3064 ,