RetrogeneDB ID: retro_cjac_2295

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:167440063..167441149(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPIRE2
• Ensembl ID: ENSCJAG00000010613
• Aliases: None
• Description: None

Sequence

>retro_cjac_2295
GAGCGGAGGCTGCGCCCAGTGCAGGGTGAGGGCTGGGCCACCTGTGGCTTTGACTCTCTGCCCTGCATCCTCAATGCCTG
CTCTGGAGACTCCAAGTCCACCTCCTGCATCAACCTGTCAGTCACAGATGCTGAGGGTAGCGCCCAGCGCCTGAGGCCCC
TTGTGCTGCTCAAGGCACCCACCTTGGCTGAGATGGAAGAGATGAACACGTCTGAGGAAGAAGAGTCTACTTGTGGGGAG
GTGACACTGACGCGGGACCGCTCCTTCTCAGAGCATGACCTGGCCCAGCTGTGAAGTGAGGTGGCCTCTGGCCTGCAGCC
GGCTACACAGCCTAAAGGAGGGACGGAGCCCCCACGGCCCCGAGCGGGCAGCGCACATGCATTGAGTCCTGGTTCCCAAG
ACCACGGTACCTATCCCACCAACCTCTCTGACCCCAGCCACCCCCTAGTCGGCAACCAGGGCTCCACGGGGAACAGACCC
AAGGCCTCCATGACACCCGATGCCAAACACCTGTGGCTGGAGTTCAGCCCCCCATGGAGAGCCTGGCCCTGACCGTGGAG
GAGGTGATGGACGTGCGCCGTGTGCTGGTGAAGGCCGAGATGGAGAAGTTTTTGCAGAACAAGGAGCTTTTCAGCAGTCT
GAAGAAGGGGAAGATCTGCTGCTGCTGCTGCCGGGCCAGGTTCCCGCTGTTCTCATGGCCGCCCACCTGTCTCCTTTGTA
AGAGAGCTGTCTGCACTTCCTGTAGCGTAAAGATGAAGATGCCTTCTAAGAGGTTTGCACACATCCCTGTCTACACGCTG
GGCTTTGAGAGTCCTCAGAGGGCGTCAGCTGCCAAAACCACGCCTGTCCAGAGAAGAGACGTCTTCCAATCTCTGCAAGG
ACCACAGTGACAGAGCGTGGAGGAGGCATTCCCCCACATCTACTCCCACGGCTGTGTCCTCAAGGACGTCTGCAGGGAGT
GCAGCAGCTTTGTGGCCGACGTGGTGCGCTCCAGCCTAAGAGCCTGGACGTCCTCAACACTACGCCACGCGAAGCCGCCA
GACCCAGTCCCTCTACATTCCTAACACCAGGACTCTTGACTTCAAG

Alignment

ORF - retro_cjac_2295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.44 %
• Parental protein coverage: 57.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ERRLRPVRGEGWATRGFGSLPCILNACSGDSKSTSCINLSVTDAGGSAQRLRPRVLLKAPTLAEMEEMNT
          ERRLRPV.GEGWAT.GF.SLPCILNACSGDSKSTSCINLSVTDA.GSAQRLRP.VLLKAPTLAEMEEMNT
Retrocopy ERRLRPVQGEGWATCGFDSLPCILNACSGDSKSTSCINLSVTDAEGSAQRLRPLVLLKAPTLAEMEEMNT

Parental  SEEEESPCGEVTLKRDRSFSEHDLAQLRSEVASGLQPATQPEGGTEPPRPRAGSAHALSPGSQDQGTYPT
          SEEEES.CGEVTL.RDRSFSEHDLAQL.SEVASGLQPATQP.GGTEPPRPRAGSAHALSPGSQD.GTYPT
Retrocopy SEEEESTCGEVTLTRDRSFSEHDLAQL*SEVASGLQPATQPKGGTEPPRPRAGSAHALSPGSQDHGTYPT

Parental  NLSDPSHPLLGNQGSTGNRPEASMTPDAKHLWLEFS-HPVESLALTVEEVMDVRRVLVKAEMEKFLQNKE
          NLSDPSHPL.GNQGSTGNRP.ASMTPDAKHLWLEFS..P.ESLALTVEEVMDVRRVLVKAEMEKFLQNKE
Retrocopy NLSDPSHPLVGNQGSTGNRPKASMTPDAKHLWLEFS<PPMESLALTVEEVMDVRRVLVKAEMEKFLQNKE

Parental  LFSSLKKGKI-CCCCRARFPLFSWPPTCLLCKRAVCTSCSIKMKMPSKKFAHIPVYTLGFESPQRASAAK
          LFSSLKKGKI.CCCCRARFPLFSWPPTCLLCKRAVCTSCS.KMKMPSK.FAHIPVYTLGFESPQRASAAK
Retrocopy LFSSLKKGKICCCCCRARFPLFSWPPTCLLCKRAVCTSCSVKMKMPSKRFAHIPVYTLGFESPQRASAAK

Parental  TTPVQRRDVFQSLQGPQWQSVEEAFPHIYSHGCVLKDVCSECSSFVADVVRSS-RKSVDVLNTTPR-RSR
          TTPVQRRDVFQSLQGPQ.QSVEEAFPHIYSHGCVLKDVC.ECSSFVADVVRSS..KS.DVLNTTPR.RSR
Retrocopy TTPVQRRDVFQSLQGPQ*QSVEEAFPHIYSHGCVLKDVCRECSSFVADVVRSS<PKSLDVLNTTPR<RSR

Parental  QTQSLYIPNTRTLDFK
          QTQSLYIPNTRTLDFK
Retrocopy QTQSLYIPNTRTLDFK

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	6.08 RPM
SRP051959_heart	0.00 RPM	0.23 RPM
SRP051959_kidney	0.02 RPM	0.42 RPM
SRP051959_liver	0.00 RPM	0.35 RPM
SRP051959_lung	0.00 RPM	2.29 RPM
SRP051959_lymph_node	0.00 RPM	0.23 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.04 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_2295 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2295 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2295 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	ENSCJAG00000010613	1 retrocopy	retro_cjac_2295 ,