RetrogeneDB ID: retro_cjac_4034

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL290005.1:2010..5106(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HRNR
• Ensembl ID: ENSCJAG00000033687
• Aliases: None
• Description: None

Sequence

>retro_cjac_4034
CAGTCTCCTAGCCGGGGCGGACACGGGTCCAGGTCGGGACAGTCTTCCAGCTACGGCCAACATGGGTCTGGCTCAGGGCA
GTCCTCTGGTTATAGTCAGCATGGAAGTGGCTCAGGGTACGGCTCTAGCCGTGGACAACATGGTTCCACGTCAGGACAGT
CCTCCAGCTTCGGCCAGGAGGGATCTAGCTCAGGTCAGTCTTCCGGCTATGGTCAGCATCGGTCTGGCTCCCGTCAGTCT
TCCAGCTACGGCCAACATGGGTCTGGCTCAGGAGAGTCCTCTGGTTATACTCAGCATGGAGGCGGCTCAGGGTCCGGCTC
TAGTCATGGACAACATGGTTCCACGTCAGGACAGTCCTCCAGCTTTGGCCAGGAGGGATCTAGCTCGGGGCAGTCTTCCA
GCTACGGTCAGCATGGCTCTGGCTCACATCAGTCTTCAGGCCGTGGCCGACACGGGTCTGGGTCTCGTTCGGGGCACTCT
TCCAGCCATGGCCCACACGGCTCTGGCTCAGGTTCTTCTTCCAGCCGAGGCCCATATGAGTCTGGCTCAGGCCACTCTTC
TGGCTTCGGTCAACATGAGTCTAGCTCAGGACAGTCCTCTGGTTCCAGTCAGCAGGGATCTGCCTCAGGTCACTCCTCTG
GCTACGGACAACATGGTTCTAGCTCAGGACAGTCACCTAGGGGCGAAGAACACGGATCTAGCTCAGGTCAGTCTTCCGGC
TATGGTCAGCATGGGTCTGCCTCCCGTCAGTCTTCAGGGCATGGACGACACGGCTCTGGATCTGGCCAGTCTCCTAGCCG
TGGCCGACATGGGTCCGGGTCGGGACAGTCTTCCAGCTACGGCCAATATGGGTCTGGCTCAGGAGAGTCCTCTGGTTACG
GTGAGCAGGGATCTGGCTCAGGTCACTCCTCTGGCTATGGACAACACGGATCTAGCTCAGGTCAGTCTTCCGGCCATGGT
CAGCATGGGTCTGCATCCCGTCAGTCTTCAGGGCATGGACGACATGGCTCTGGAGCTGGCCAGTCTCCTAGCCGCGGCCG
ACATGGGTCCGGGTCGGGACAGTCTTCCAGCTACGGCCAACATGGGTCTGGCTCAGGACAGTCCTCTGGTTATAGTCAGC
ACGGAAGTGGCTCAGGGTATGGCTCTAGCCGTGGACAACATGGTTCCACGTCAGGACAGTCCTCCAGCTTCGGCCAGGAG
GGATCTAGCTCAGGTCAGTCTTCCGGCTATGGTCAGCATCGGTCTGGCTCCCGTCAGTCTTCCAGCTACGGCCAACATGG
ATCTGGCTCAGGAGAGTCCTCTGGTTATAGTCAGCACGGAGGCGGCTCAGGGTCCGGCTCCAGTCATGGACAACATGGTT
CCACGTCAGAACAGTCCTCCAGCTTTGGTCAGGAGGGATCTAGCTCGGCGCAGTCTTCCAGCTACGGTCAGCATGGCTCT
GGCTCACATCAGTCTTCCTGCCGCGGCCGACACGAATCTGGATCTGGTTCGGGGCACTCTTCCAGCCATGGCCCACACGG
CTCTGGCTCAGGTTCTTCTTCCAGCCGAGGCACATATGAGTCTGGCTCAGGCCACTCTTCTGGCTTCGGTCAACGTGAGT
CTAGCTCAGGAGAGTCCTCTGGTTCCAATCAGCAGGGATCTGCCTCAGGTCACTGCTCTGCCTACGGACAACATGGTTCT
AGCTCAGGACTGTCTCCGAGGGGTGAACAACACGGATCTAGCTCAGGTCAGTCTTCCGGCCATGGTCAGCATGGGTCTGG
CTCCCGTCAGTCTTCGGGCCATGGCCGACGCGGCTCTGGATCTGGCCAGTCTCCTAGCCGGGGCGGACATGGGTCCAGGT
CAGGACAGTCTTCCAGCTACGGCCAATATGGGTCTGGCTCAGGAGAGTCCTCTGGTTACGGTGAGCAGGGATCTGGCTCA
GGTCACTCCTCTGGCTATGGACAACACGGATCTAGCTCAGGTCAGTCTTCCGGCTATGGTCAGCATGGGTCTGCCTCCCG
TCAGTCTTCAGGCCATGGCCGACATGCGTCTGGATCTGGCCAGTCCCCTAGCCCTGGCCGCGGCCGACATGGATCTGGTT
CTGGGCAGTCTTCCAGCTACGGCCCACATGGGTCTGGCTCAGGGCAGTCTTCCAGCCGTGGCCCATATGAGTCTGGCTCA
GGTCACTCTTCTGGTGTAGGTCAACATGAGTCTCGTTCAGGACAGTCCTCTGGCTACGCTCAACGCGGATCTAGCTCGGG
TCATTCCTCTAGCCGTGGACAGCATGGTTCTACATCAGGACAGTCATCAAGCTGTGAACAACATGGAGCTAGCTCAGGTC
AGTCCTCCAGCTATGGCAACCATGGCTCCGGCTCAAGTCAGTCTTCTGGCTATGGCCGACACGGCTCTGGATCTGGCCAG
TCTCCTAGCCGTGGCCGACATGGGTCCGGGTCAGGACAGTCCTCTGGTTATAGTCAGCATGGAAGTGGCTCAGGGTACGG
CTCTAGCCATGGACAACATGGTTCCACGTCAGGACAGTCCTCCAGCTTTGGCCAGGAGGGATCTAGCTCGGGGCAGTCTT
CCAGCTACGGTCAGCATGGCTCTGGCTCACATCAGTCTTCGGGCCGCGGCCAACACGGGTCTGGGTCTCGTTCGGGGCAC
TCTTCCAGCCATGGCCCACACGGCTCTGGCTCAGGTTCTTCTTCCAGCCGAGGCCCATATGAGTCTGGCTCAGGCCACTC
TTCTGGCTTCGGTCAACATGAGTCTAGCTCAGGACAGTCCTCTGGTTCCAGTCAGCAGGGATCTGCCTCAGGTCACTCCT
CTGGCTACGGACAACATGGTTCTAGCTCAGGACTGTCACCTAGGGGCGAACAACACGGATCTAGCTCAGGTCAGTCTTCT
GGCTATGGTCAGCATGGGTCTGCCTCCCGTCAGTCTTCAGGGCATGGACGACACGGCTCTGGATCTGGCCAGTCTCCTAG
CCGTGGCCGACATGGGTCCGGGTCGGGACAGTCTTCCAGCTACGGCCAACATGGGTCTGGCTCAGGGCAGTCCTCTGGTT
ATAGTCAGCATGGAAGTGGCTCAGGGTATGGCTCTAGCCGTGGACAACATGGTTCC

Alignment

ORF - retro_cjac_4034 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.02 %
• Parental protein coverage: 82.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSSGSSQQGSASGHCSAYGQHGSSSGLSPRGEQPGSSSGQSSGHGQHGSGSRQSSGHGRRGSGSGQSPSR
          QS......GS.SG..S.YGQHGS.SG.S....Q.GS.SG..S..GQHGS.S.QSS..G..GS.SGQS...
Retrocopy QSPSRGGHGSRSGQSSSYGQHGSGSGQSSGYSQHGSGSGYGSSRGQHGSTSGQSSSFGQEGSSSGQSSGY

Parental  GGHGSRSGQSSSYGQYGSGSGESSGYGEQGSGSGHSSGYGQHGSSSGQSSGYGQHGSASRQSSGHGQHGS
          G.H.S.S.QSSSYGQ.GSGSGESSGY...G.GSG..S..GQHGS.SGQSS..GQ.GS.S.QSS..GQHGS
Retrocopy GQHRSGSRQSSSYGQHGSGSGESSGYTQHGGGSGSGSSHGQHGSTSGQSSSFGQEGSSSGQSSSYGQHGS

Parental  GAGHSGQSSGYGQHRSGSHQ--SSGHGRHGSGSGQSPSRGQHGSGSG---GRGQHGSTSGQSSSCEQHGA
          G...S.QSSG.G.H.SGS....SS.HG.HGSGSG.S.SRG...SGSG...G.GQH.S.SGQSS...Q.G.
Retrocopy G---SHQSSGRGRHGSGSRSGHSSSHGPHGSGSGSSSSRGPYESGSGHSSGFGQHESSSGQSSGSSQQGS

Parental  SSGQSSSYGNHGSGSSQSSGYGRHGSGSGQSPSRGRHGSGSGQSSGYSQHGSGSGYSSSHGQHGSTSGQS
          .SG.SS.YG.HGS.S.QS.....HGS.SGQS...G.HGS.S.QSSG...HGSGSG.S.S.G.HGS.SGQS
Retrocopy ASGHSSGYGQHGSSSGQSPRGEEHGSSSGQSSGYGQHGSASRQSSGHGRHGSGSGQSPSRGRHGSGSGQS

Parental  SSFGQEGSSSGQSSSYGQHGSGSHQSSGRGQHGSGSGQSSGYGQHRSGSRQSSSYGQHGSGSGESSGYSQ
          SS.GQ.GS.SG.SS.YG..GSGS..SSG.GQHGS.SGQSSG.GQH.S.SRQSS..G.HGSG.G.S.....
Retrocopy SSYGQYGSGSGESSGYGEQGSGSGHSSGYGQHGSSSGQSSGHGQHGSASRQSSGHGRHGSGAGQSPSRGR

Parental  HGGGSGSGSSHGQHGSTSGQSSSYGQYGSGSGESSGYGEQGSGSGHSSGYGQHGSSSGQSSGYGQHGSAS
          HG.GSG..SS.GQHGS.SGQSS.Y.Q.GSGSG..S..G..GS.SG.SS..GQ.GSSSGQSSGYGQH.S.S
Retrocopy HGSGSGQSSSYGQHGSGSGQSSGYSQHGSGSGYGSSRGQHGSTSGQSSSFGQEGSSSGQSSGYGQHRSGS

Parental  RQSSGYGQHRSGSRQSSGHGRHGSGSGQSPSRGQHGSGSGGSSSYGQYGSGSGQSSGYGEQGSGSGHSSG
          RQSS.YGQH.SGS..SSG...HG.GSG...S.GQHGS.S..SSS.GQ.GS.S.QSS.YG..GSGS..SS.
Retrocopy RQSSSYGQHGSGSGESSGYSQHGGGSGSGSSHGQHGSTSEQSSSFGQEGSSSAQSSSYGQHGSGSHQSSC

Parental  YGQH--GSSSGQYSGYGQHGSGSRQSPSFGQEGSSSGQSSSYGQHGSGSHQSSGRGQHGSGSRHSSGFGQ
          .G.H..GS.SG..S..G.HGSGS..S.S.G...S.SG.SS..GQ..S.S..SSG..Q.GS.S.H.S..GQ
Retrocopy RGRHESGSGSGHSSSHGPHGSGSGSSSSRGTYESGSGHSSGFGQRESSSGESSGSNQQGSASGHCSAYGQ

Parental  HESSSGQS-SGSKHGSSSGQSSGYGQHGSASRQSSGHGRHGSGSGQSPSRGRHGSGSGQSSSYGQYGSGS
          H.SSSG.S..G..HGSSSGQSSG.GQHGS.SRQSSGHGR.GSGSGQSPSRG.HGS.SGQSSSYGQYGSGS
Retrocopy HGSSSGLSPRGEQHGSSSGQSSGHGQHGSGSRQSSGHGRRGSGSGQSPSRGGHGSRSGQSSSYGQYGSGS

Parental  GESSGYGEQGSGSGHSSGYGQHGSSSGQSSGHGQHGSASRQSSGHGQHGSGAGQSPS--RGRHGSGSGQS
          GESSGYGEQGSGSGHSSGYGQHGSSSGQSSG.GQHGSASRQSSGHG.H.SG.GQSPS..RGRHGSGSGQS
Retrocopy GESSGYGEQGSGSGHSSGYGQHGSSSGQSSGYGQHGSASRQSSGHGRHASGSGQSPSPGRGRHGSGSGQS

Parental  SSYGQHGSGSGQSSGYSQHGTSSGQSSSYGNHGSGSSQSSGYGRHGSGSGQSPSRGRHGSGSGQSSGYSQ
          SSYG.HGSGSGQSS........SG.SS..G.H.S.S.QSSGY...GS.SG.S.SRG.HGS.SGQSS...Q
Retrocopy SSYGPHGSGSGQSSSRGPYESGSGHSSGVGQHESRSGQSSGYAQRGSSSGHSSSRGQHGSTSGQSSSCEQ

Parental  HGSGSGYSSSHGQHGSTSGQSSSFGQEGSSSGQSSSYGQHGSGSHQSSGRGQHGSGSGQSSGYGQHGSAS
          HG..SG.SSS.G.HGS.S.QSS..G..GS.SGQS.S.G.HGSGS.QSSG..QHGSGSG..S..GQHGS.S
Retrocopy HGASSGQSSSYGNHGSGSSQSSGYGRHGSGSGQSPSRGRHGSGSGQSSGYSQHGSGSGYGSSHGQHGSTS

Parental  RQSSGHGRHGSGSGQSPSRGRHGSGSGQSSSYGQYGSG--SGESSGYGEQGSGSGHSSGYGQHGSSSGQS
          .QSS..G..GS.SGQS.S.G.HGSGS.QSS..GQ.GSG..SG.SS..G..GSGSG.SS..G...S.SG.S
Retrocopy GQSSSFGQEGSSSGQSSSYGQHGSGSHQSSGRGQHGSGSRSGHSSSHGPHGSGSGSSSSRGPYESGSGHS

Parental  SGHGQHGSASRGSSSYGQYGSGSGQSSGYGEQGSGSGHSSGYGQHGSSSGQSSGYGQHGSGSRQSSGHGR
          SG.GQH.S.S..SS...Q.GS.SG.SSGYG..GS.SG.S....QHGSSSGQSSGYGQHGS.SRQSSGHGR
Retrocopy SGFGQHESSSGQSSGSSQQGSASGHSSGYGQHGSSSGLSPRGEQHGSSSGQSSGYGQHGSASRQSSGHGR

Parental  HASGSGQSPSPGRGRHGSGSGQSSSYGPHGSGSGQSSSRGPYESGSGHSSGVGQHES
          H.SGSGQSPS..RGRHGSGSGQSSSYG.HGSGSGQSS......SGSG..S..GQH.S
Retrocopy HGSGSGQSPS--RGRHGSGSGQSSSYGQHGSGSGQSSGYSQHGSGSGYGSSRGQHGS

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	0.09 RPM	0.16 RPM
SRP051959_heart	0.09 RPM	0.26 RPM
SRP051959_kidney	0.00 RPM	0.16 RPM
SRP051959_liver	0.43 RPM	1.41 RPM
SRP051959_lung	0.34 RPM	0.80 RPM
SRP051959_lymph_node	0.34 RPM	1.28 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	1.30 RPM	4.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4034 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4034 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4034 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	ENSCJAG00000033687	1 retrocopy	retro_cjac_4034 ,