RetrogeneDB ID: retro_cjac_144

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:126863916..126865905(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000035174
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007193
• Aliases: None
• Description: None

Sequence

>retro_cjac_144
AGCTCGACGCTTCAGAGGCGACGCGAGATGGCGGCAGCGACGGCGACCTCAGGAGCTGGTCGCTGTCGGCTAAGCAAGAT
AGGAGCTAGTCGTCGCCCACCTCCAGCTCGCCTAAGGGTGGCTGTGCGACTGCGGCCATTTGTGGATAGAACAGCTGGAA
CAAGCGATCCCCCCTGTGTGCGGGGCATGGACAGCTGCTCTCTAGAGATTGCTAACTGGAGGAACCACCAGGAGACTCTC
AAATACCAGTTTGATGCCTTCTATGGGGAGAGGAGTACTCAGCAGGACATCTACACAGGTTCAGTGCAGCCCATCCTAAG
GCACTTGCTAGAAGGACAGAATGCCAGTGTGCTTGCCTATGGACCCACAGGAGCTAGGAAGACACACACAATGCTGGGCA
GCCCGGAGCAACCTGGGGTGATCCCACGGGCTCTCATGGACCTCCTGCAGCTCACAAGGGAGGAGGGCACCGAGGGCCGG
CCATGGGCCCTGTCTGTCACCATGTCCTACTTAGAGATCTACCAGGAGAAGGTATTAGACCTCCTGGACCCTGCATCAGG
AGACCTGGTGATCCGAGAAGACTGCCGGGGGAACATCCTGATTCCGGGCCTCACGCAGAAGCCCATCACTAGCTTTGCTG
ATTTTGAGCGGCACTTCCTGCCAGCCAGTCGAAACCGGACTGTAGGTGCCACCCGGCTCAACCAGCGCTCCTCCCGCAGT
CACGCTGTGCTCCTGGTCAAGGTGGACCAGCGGGAACGTTTGACCCCATTTCGCCAGCGAGAGGGAAAACTCTACCTCAT
TGACTTGGCTGGGTCAGAGGACAACCGTCGCACAGGCAACAAGGGCCTTCGGCTAAAAGAGAGCGGAGCCATCAACACCT
CCCTGTTTGTCCTGGGCAAGGTGGTGGATGCGCTGAATCCGGGCCTTCCTCGTGTACCTTACCAAGATAGCAAGCTCACT
CGCCTACTGCAGGACTCTCTGGGTGGCTCAGCTCACAGCATCCTTATTGCCAACATTGCCCCTGAGAGACGCTTCTACCT
AGACACCGTCTCCGCACTCAACTTCGCTGCCAGGTCTAAGGAGGTGATCAACCGGCCTTTTACCAATGAAAGCCTGCAGC
CTCCCGTCTTGGCACCTGTTAAGCTGTCTCAGAAAGAATTCCTTGGTTCACCAGAGGCAAAGAGAGCCCGAGGCCCTGAG
GAAGAGGAGATTGGGAGCCCTGAGCCCATGGCAGCTCCAGCCTCTGCCTCACAGAAACTCAGCCCCCTACAGAAGCTAAG
CAGCATGGACCCGGCCATGCTGGAGCGCCTCCCGAGCTTGGACCATCTGCTGGCCTCCCAGGGGAGCCAGGGGGTCCCTC
TGTTGAGTACCCCAAAGCGAGAGCGGATGGTGCTCATGAAGACAGTGGAAGAGAAGGACTTGGAGATTGAGAGGCTTAAG
ATGAAGCAAAAAGAACTGGAGGCCAAGATGTTGGCCCAAAAGGCTGAAGACTCAAAGGCAAAGGAGAACCCTTATCCCAC
AATGCTCCGGCCCTCTTCGCATCGCACAGTCACAGTGGCAAAGCCCCTGAAAAAGGCTGTGGTGATGCCCCTACAGCTAA
TTCAGGAGCAGGCAGCATCCCCAAATGCCGAGATCCATATCCTGAAGAATAAAGGCCGGAAGAGAAAGCTGGAGTCCCTG
GATGCCTCAGAGCCTAAGGAGAAGGCAGAGGACTGCTGGGAGCTACAGATCAGCCCAGAGCTTTTGGCTCATGGGCGCAA
AAAAATACTGGATCTGCTGAAGGAAGGCTCAGCCAGGGATCTCCGCAGTCTTCAGCGCATTGGCCCGAAGAAGGCCCAGC
TCATCGTGGGCTGGCGGGAGCTCCACGGCCCCTTCAGCCAGGTGGAGGACCTGGAACGCATGGAGGGCATAACAGGGAAA
CAGATGGAGTCCTTCCTGAAGGCGAACATCCTAGGTCTCGCCGCCGGCCAGCGCTGTGACCCGTCTTGA

Alignment

ORF - retro_cjac_144 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.29 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STLQRRREMAAATATSVXGAGRCRLSKIGASRRPPPARVRVAVRLRPFVDRTAGTSDPPCVRGMDSCSLE
          STLQRRREMAAATATS..GAGRCRLSKIGASRRPPPAR.RVAVRLRPFVDRTAGTSDPPCVRGMDSCSLE
Retrocopy STLQRRREMAAATATS--GAGRCRLSKIGASRRPPPARLRVAVRLRPFVDRTAGTSDPPCVRGMDSCSLE

Parental  IANWRNHQETLKYQFDAFYGERSTQQDIYTGSVQPILRHLLEGQNASVLAYGPTGAGKTHTMLGSPEQPG
          IANWRNHQETLKYQFDAFYGERSTQQDIYTGSVQPILRHLLEGQNASVLAYGPTGA.KTHTMLGSPEQPG
Retrocopy IANWRNHQETLKYQFDAFYGERSTQQDIYTGSVQPILRHLLEGQNASVLAYGPTGARKTHTMLGSPEQPG

Parental  VIPRALMDLLQLTREEGTEGRPWALSVTMSYLEIYQEKVLDLLDPASGDLVIREDCRGNILIPGLTQKPI
          VIPRALMDLLQLTREEGTEGRPWALSVTMSYLEIYQEKVLDLLDPASGDLVIREDCRGNILIPGLTQKPI
Retrocopy VIPRALMDLLQLTREEGTEGRPWALSVTMSYLEIYQEKVLDLLDPASGDLVIREDCRGNILIPGLTQKPI

Parental  TSFADFERHFLPASRNRTVGATRLNQRSSRSHAVLLVKVDQRERLTPFRQREGKLYLIDLAGSEDNRRTG
          TSFADFERHFLPASRNRTVGATRLNQRSSRSHAVLLVKVDQRERLTPFRQREGKLYLIDLAGSEDNRRTG
Retrocopy TSFADFERHFLPASRNRTVGATRLNQRSSRSHAVLLVKVDQRERLTPFRQREGKLYLIDLAGSEDNRRTG

Parental  NKGLRLKESGAINTSLFVLGKVVDALNQGLPRVPYRDSKLTRLLQDSLGGSAHSILIANIAPERRFYLDT
          NKGLRLKESGAINTSLFVLGKVVDALN.GLPRVPY.DSKLTRLLQDSLGGSAHSILIANIAPERRFYLDT
Retrocopy NKGLRLKESGAINTSLFVLGKVVDALNPGLPRVPYQDSKLTRLLQDSLGGSAHSILIANIAPERRFYLDT

Parental  VSALNFAARSKEVINRPFTNESLQPPVLAPVKLSQKEFLGPPEAKRARGPEEEEIGSPEPMAAPASASQK
          VSALNFAARSKEVINRPFTNESLQPPVLAPVKLSQKEFLG.PEAKRARGPEEEEIGSPEPMAAPASASQK
Retrocopy VSALNFAARSKEVINRPFTNESLQPPVLAPVKLSQKEFLGSPEAKRARGPEEEEIGSPEPMAAPASASQK

Parental  LSPLQKLSSMDPAMLERLLSLDRLLASQGSQGVPLLSTPKRERMVLMKTVEEKDLEIERLKMKQKELEAK
          LSPLQKLSSMDPAMLERL.SLD.LLASQGSQGVPLLSTPKRERMVLMKTVEEKDLEIERLKMKQKELEAK
Retrocopy LSPLQKLSSMDPAMLERLPSLDHLLASQGSQGVPLLSTPKRERMVLMKTVEEKDLEIERLKMKQKELEAK

Parental  MLAQKAEDSKEKENHYPTMLRPLSHRTVTMAKPLKKAVVMPLQLIQEQAASPNAEIHILRNKGRKRKLES
          MLAQKAEDSK.KEN.YPTMLRP.SHRTVT.AKPLKKAVVMPLQLIQEQAASPNAEIHIL.NKGRKRKLES
Retrocopy MLAQKAEDSKAKENPYPTMLRPSSHRTVTVAKPLKKAVVMPLQLIQEQAASPNAEIHILKNKGRKRKLES

Parental  LDASEPEEKAEDCWELQISPELLAHGRKKILDLLNEGSARDLRSLQRIGPKKAQLIVGWRELHGPFSQVE
          LDASEP.EKAEDCWELQISPELLAHGRKKILDLL.EGSARDLRSLQRIGPKKAQLIVGWRELHGPFSQVE
Retrocopy LDASEPKEKAEDCWELQISPELLAHGRKKILDLLKEGSARDLRSLQRIGPKKAQLIVGWRELHGPFSQVE

Parental  DLERVEGITGKQMESFLKANILGLAAGQRCDLS
          DLER.EGITGKQMESFLKANILGLAAGQRCD.S
Retrocopy DLERMEGITGKQMESFLKANILGLAAGQRCDPS

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	0.16 RPM	7.72 RPM
SRP051959_heart	0.00 RPM	1.68 RPM
SRP051959_kidney	0.16 RPM	1.06 RPM
SRP051959_liver	0.00 RPM	0.58 RPM
SRP051959_lung	0.02 RPM	1.90 RPM
SRP051959_lymph_node	0.07 RPM	4.50 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.98 RPM
SRP051959_spleen	0.06 RPM	3.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_144 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007193	1 retrocopy	retro_cjac_144 ,
Mus musculus	ENSMUSG00000030677	1 retrocopy	retro_mmus_471,
Otolemur garnettii	ENSOGAG00000000266	1 retrocopy	retro_ogar_2234,
Pteropus vampyrus	ENSPVAG00000017206	1 retrocopy	retro_pvam_313,