RetrogeneDB ID: retro_cjac_295

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:25828998..25829724(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021835
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000018474
• Aliases: None
• Description: None

Sequence

>retro_cjac_295
ATGTCCGGGGAGTCAGCCAGGAGCCTGGGGAAGGGAAGCGCGCCCCCAGGGCCGGTCCCAGAGGGCCTGATCCGCGTCTA
CAGCATGAGGTTCTGCCCGTTTGTTGAGAGGACGCGTCTGGTCCTGAAGGCCAAGGGAATCAGGCATGAAGTCATCAATA
TCAACCTGAAAAATAAGCCTGAGTGGTTCTTTAAGAAAAATCCCTTTGGTCTGGTGCCAGTTTTGGAAAACAGTCAGGGT
CAGCTGATCTACGAGTCTGCCATCACTTGTGAGTACCTGGATGAAGCATACCCAGGGAAGAAGCTGTTTCCTGATGACCC
CTATGAGAAAGCTTGCCAGAAGATGGTCTTCGAGTTGTTTTCTAAGGTGCCATCCTTGGTAGGAAGCTTTATTAGAAGCC
AAAATAAGGAAGACTGTGCTGGCCTAAAAGAAGAATTTCGTAAAGAATTTAGCAAGCTGGAGAAGGTTCTGACTAATAAG
AAGACAACCTTCTTTGGTGGCAGTTCTATCTCGATGATTGATTACCTCATCTGGCCCTGGTTTGAACGGCTGGAAGCAAT
GAAGTTAAATGAGTGTGTAGATCACACTCCAAAACTTAAACTGTGGATGGCAGCCATGAAGGAAGATCCCACAGTCTCAG
CCCTGCTCACTAGTGTGAAGGACTGGCAAGGTTTCCTAGAGCTGTACTTACAGAACAGCCCTGAGGCCTGTGATTATGGG
CTCTGA

Alignment

ORF - retro_cjac_295 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGESARSLGKGSAPPGPVPEGLIRVYSMRFCPFAERTRLVLKAKGIRHEVININLKNKPEWFFKKNPFG
          MSGESARSLGKGSAPPGPVPEGLIRVYSMRFCPF.ERTRLVLKAKGIRHEVININLKNKPEWFFKKNPFG
Retrocopy MSGESARSLGKGSAPPGPVPEGLIRVYSMRFCPFVERTRLVLKAKGIRHEVININLKNKPEWFFKKNPFG

Parental  LVPVLENSQGQLIYESAITCEYLDEAYPGKKLFPDDPYEKACQKMVFELFSKVPSLVGSFIRSQNKEDCA
          LVPVLENSQGQLIYESAITCEYLDEAYPGKKLFPDDPYEKACQKMVFELFSKVPSLVGSFIRSQNKEDCA
Retrocopy LVPVLENSQGQLIYESAITCEYLDEAYPGKKLFPDDPYEKACQKMVFELFSKVPSLVGSFIRSQNKEDCA

Parental  GLKEEFRKEFSKLEKVLTNKKTTFFGGSSISMIDYLIWPWFERLEAMKLNECVDHTPKLKLWMAAMKEDP
          GLKEEFRKEFSKLEKVLTNKKTTFFGGSSISMIDYLIWPWFERLEAMKLNECVDHTPKLKLWMAAMKEDP
Retrocopy GLKEEFRKEFSKLEKVLTNKKTTFFGGSSISMIDYLIWPWFERLEAMKLNECVDHTPKLKLWMAAMKEDP

Parental  TVSALLTSVKDWQGFLELYLQNSPEACDYGL
          TVSALLTSVKDWQGFLELYLQNSPEACDYGL
Retrocopy TVSALLTSVKDWQGFLELYLQNSPEACDYGL

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	0.27 RPM	15.97 RPM
SRP051959_heart	0.18 RPM	3.03 RPM
SRP051959_kidney	0.18 RPM	6.74 RPM
SRP051959_liver	0.17 RPM	9.75 RPM
SRP051959_lung	0.28 RPM	6.02 RPM
SRP051959_lymph_node	0.25 RPM	5.96 RPM
SRP051959_skeletal_muscle	0.20 RPM	1.90 RPM
SRP051959_spleen	0.25 RPM	3.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_295 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_295 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_295 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018474	1 retrocopy	retro_cjac_295 ,
Echinops telfairi	ENSETEG00000017967	1 retrocopy	retro_etel_1413,
Homo sapiens	ENSG00000148834	1 retrocopy	retro_hsap_2704,
Gorilla gorilla	ENSGGOG00000005064	1 retrocopy	retro_ggor_24,
Macaca mulatta	ENSMMUG00000015334	1 retrocopy	retro_mmul_142,
Nomascus leucogenys	ENSNLEG00000015358	1 retrocopy	retro_nleu_1577,
Pongo abelii	ENSPPYG00000002633	1 retrocopy	retro_pabe_2256,
Pan troglodytes	ENSPTRG00000002925	1 retrocopy	retro_ptro_1825,