RetrogeneDB ID: retro_cjac_1383

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:20551860..20553387(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRAME
• Ensembl ID: ENSCJAG00000020319
• Aliases: None
• Description: None

Sequence

>retro_cjac_1383
ATGGAACGAAGGCATTTTCGGACTTACATTCAGAGCCGATTCATCAGCATGAGCATGTGGACGAGCCCACGGAGACTCGT
GGACCTGGCGGGGCAGAGCCTGCTGAAGAATGAGGCCCTGGCCATCGCTGCCCTGGAGTTGCTCCCCAGGGAGCTCTTCC
CGCCGCTCTTCACGGCAGCCTTTGACGGGAGACACAACCAGACCCTGAAGGCCATGGTGCAGGCCTAGCCCTTCACCTGC
CTCCCTCTGGGAGTGCTGATGAAGGGACAGCAGCTTCACGTGGAGACCTTCAAAGCTGTGCTTGATGGAGTTGATGTGCT
GCTTGCCCAGGAGGTTCGCCCCAGGAGGTGGACACTCAAAGTGCTGGATTTACGAAAGAATTCTCATCAAGACTTCTGGA
CCGTGTGGTCTGGAAAAAGGGTCAGTCTGTGCTCATTTCCAGAGCCAGAAGCAGCTCAGCCCATGAGAAAGAAGCGAAAA
GTAGATGGTTCGAGCACAGAGGCAGGGCAGCGCTTTATTCCAATAGAGGCTCTCGTAGACCTGTCCCTCAAGGAAGGTGC
CTATGATGAATTGTTCATCCACCTGATTGAGATAGTGAGGAGAAAGAAAGACGTACTACACCTGTGCTGTAAGAAGCTGA
AGATTTTTGCAATGTCTGTGCAGAATATCAAGATGATCCTGAAAATGGTGCAGCTGGACTCTATTGAAGATTTGGAAGTG
ACTTGCACCTGGAAACTACCCACCTCGGCGAAATTTTCTCCTCACCTGAGCCAGATGAGTAATCTGCGTAGACTGCTCCT
CGCCCACAACCATCCGTCTTCCTTCATTTCCCCGGAGAAGGAGGAGCAGTTTATCGCCCAGTTCATCTCTCAGTTCCTCA
ATCTCCACTGCCTTGAGGAGCTCTATGTGGACTCTTTATTTTTCCTCAGAGGCCACCTGGATCAGTTGCTCAGATGCATG
ATGAACCCGTTGGAAACCCTCTCGATAACTAACTGCTGGCTTTCAGAAGAAGATGTGACACATCTGTCCCAGAGCCCCAA
CATCAGTCAGCTGAGTGTCCTGAGTCTAAGTGGGGTCATGCTGACCGAGATAAATCCCGAGCTCCTCCAAGCTCTGCTAG
AGAGAACCTCCGCCACCCTCCAGGACCTGGACTTAGATGAGTGTGGAATCGTGGATACTCAGCTCCTTGTTCTTCTGCCT
TCCCTGAGCCACTGCTCCCAGCTTACCACCTTCAGCTTCTGCGGGAATCCCATCTCCATGTCTGTCCTGGAGAGCCTCGT
GCACCACATCATCGGGTTGAATAATCTGAGCCACGTGCTGTATCCTGTCCCCGTGGAGAGCTTTGAGGACATCAATGGCA
CCCTCGACCTGGGGAGACTTGCCTATCTGCACACCAGGCTTAGGGAGTTGCTATGCGAATTGGGACGGCCTGGCATGGTC
TGGCTCAGTGCCACCCCCTGTCCTCACTGTGGGGACAGAACCTTCTATGACCCAGATCCTATCCTGTGCCCCTGTTTCAT
GCCTGCC

Alignment

ORF - retro_cjac_1383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERRHLRTYIQSRFISMSMWTSPRRLVDLAGQSLLKNESLAIAALELLPRELFPPLFTAAFDGRHNKTLK
          MERRH.RTYIQSRFISMSMWTSPRRLVDLAGQSLLKNE.LAIAALELLPRELFPPLFTAAFDGRHN.TLK
Retrocopy MERRHFRTYIQSRFISMSMWTSPRRLVDLAGQSLLKNEALAIAALELLPRELFPPLFTAAFDGRHNQTLK

Parental  AMVQAWPFTCLPLGVLMKGQQLHVETFKAVLDGVDVLLAQEVRPRRWKLKVLDLRKNSHQDFWTVWSGKR
          AMVQA.PFTCLPLGVLMKGQQLHVETFKAVLDGVDVLLAQEVRPRRW.LKVLDLRKNSHQDFWTVWSGKR
Retrocopy AMVQA*PFTCLPLGVLMKGQQLHVETFKAVLDGVDVLLAQEVRPRRWTLKVLDLRKNSHQDFWTVWSGKR

Parental  VSLCSFPEPEAAQPMRKKRKVDGSSTEAEQRFIPIEVLVDLSLKEGAYDELFIHLIEIVRRKKDVLHLCC
          VSLCSFPEPEAAQPMRKKRKVDGSSTEA.QRFIPIE.LVDLSLKEGAYDELFIHLIEIVRRKKDVLHLCC
Retrocopy VSLCSFPEPEAAQPMRKKRKVDGSSTEAGQRFIPIEALVDLSLKEGAYDELFIHLIEIVRRKKDVLHLCC

Parental  KKLKIFAMPVQNIKMILKMVQLDSIEDLEVTCTWKLPTLAKFSPHLSQMSNLRRLLLAHIHPASFISPEK
          KKLKIFAM.VQNIKMILKMVQLDSIEDLEVTCTWKLPT.AKFSPHLSQMSNLRRLLLAH.HP.SFISPEK
Retrocopy KKLKIFAMSVQNIKMILKMVQLDSIEDLEVTCTWKLPTSAKFSPHLSQMSNLRRLLLAHNHPSSFISPEK

Parental  EEQFIAQFISQFLNLHCLEELYVDSLFFLRGHLDQLLRCMMNPLETLSITNCWLSEEDVTHLSQSPNISQ
          EEQFIAQFISQFLNLHCLEELYVDSLFFLRGHLDQLLRCMMNPLETLSITNCWLSEEDVTHLSQSPNISQ
Retrocopy EEQFIAQFISQFLNLHCLEELYVDSLFFLRGHLDQLLRCMMNPLETLSITNCWLSEEDVTHLSQSPNISQ

Parental  LSVLSLSGVMLTEINPELLQALLERTSATLQDLDLDECGIVDTQLLVLLPSLSHCSQLTTFSFCGNPISI
          LSVLSLSGVMLTEINPELLQALLERTSATLQDLDLDECGIVDTQLLVLLPSLSHCSQLTTFSFCGNPIS.
Retrocopy LSVLSLSGVMLTEINPELLQALLERTSATLQDLDLDECGIVDTQLLVLLPSLSHCSQLTTFSFCGNPISM

Parental  SVLESLVHHIIGLNNLSHVLYPVPVESFEDINGTLDLGRLAYLHTRLRELLCELGRPGMVWLSATPCPHC
          SVLESLVHHIIGLNNLSHVLYPVPVESFEDINGTLDLGRLAYLHTRLRELLCELGRPGMVWLSATPCPHC
Retrocopy SVLESLVHHIIGLNNLSHVLYPVPVESFEDINGTLDLGRLAYLHTRLRELLCELGRPGMVWLSATPCPHC

Parental  GDRTFYDPDPILCPCFMPA
          GDRTFYDPDPILCPCFMPA
Retrocopy GDRTFYDPDPILCPCFMPA

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	0.20 RPM
SRP051959_heart	0.02 RPM	0.19 RPM
SRP051959_kidney	0.04 RPM	0.18 RPM
SRP051959_liver	0.02 RPM	0.26 RPM
SRP051959_lung	0.02 RPM	0.31 RPM
SRP051959_lymph_node	0.02 RPM	0.32 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.09 RPM
SRP051959_spleen	0.00 RPM	0.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1383 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1383 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020319	2 retrocopies	retro_cjac_1383 , retro_cjac_2512,