RetrogeneDB ID: retro_cjac_444

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:87213530..87215253(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MVP
• Ensembl ID: ENSCJAG00000007166
• Aliases: None
• Description: None

Sequence

>retro_cjac_444
GGCATCCAGGATGTGTACATGCTGTCAGAGCAGGAGGGGCTGCTGCTGAGGGCCCTGCAGCCCCTGGAGGACGGGGAGGA
TGTGGAGAAGGTCTCACGCCAGGCTGGGGACCACTGGCTCATCCGCGGACTCCTGGAGTACGTGCCATCTGCCAAGGTGG
AGGTGGTGGAGGAGCGCCAGGCCATCCCTCTAGATGAGAACGAGGGCATCTATGTGCAGGGTGTTGAGACGGGAAAGGTG
TGGGCCGTGATCGGAAGCACCTACATGCTGATGGAGGATGAAGTCCTGTGGGAGAAGGAGCTGCCTCCCGGGGTGGAGGA
GCTGCTCAACAAGGGGCAGGACCCCTCTGGCAGACAGGGGTGACAAGGGCACAGCTAAGAGCCTCCAGCCCTCCACGCCC
CGGAACAAGACCCATGTGGTCAGCTACCGCGTGCCCCACAACGCTGCCGTGCAGGTGTATGACTACCGAGCGAAGTGAGC
CCGTGTGGTCTTTGGGCCTGAGCTGGTGTCGCTGGGTCCTGAGGAGCATTTCATGGTGCTGTCCCTTTCGGCCGGGTGGC
CCAAGTGTCCCCATGCCCACCGTGCGCTCTGCCTGCTTCTTGGGCCTGACTTCTTCACAGACGTCACCACCATTGAAACA
GCGGATCATGCCAGGCTGCAACTGCAGCTGGCCTACAATTGGCACTTCGAGGTGAATGACCGGAAGGACCCCCAAGAGAC
AGCCAAGCTCTTTTCTGTGCCAGACTTTGTAGGTGACGCCTGCAAGGCCATCGCATCCTGGGTACGGGGAGGCTGTGGCC
TCTCACTTTCGATGATTTCCATAAGAACTCGGCCCGCATCATTCGCACTGCCGTCTTTGGCTTTGAGACCTCGGAAGCCA
AGGGCCCCGATGGCATAACCCTGCCCAGGCCCCGGGATCGGGCTGTCTTCTCCCAAAATGGGCTGGTGGTCAGGAGCATG
GATGTGTAGTCAGTAGAGCCCGTGGACCAGAGAACCCGGGACGCCCTGCAACGTAGTGTCTAGCTGGCCATTGAGATCAC
CACCAACTCCCAGGAAGCGGCAACCAAGCACGAGGCTCAGAGACTGGAGCAGGAAGCCCGCAGCCGACTTGAGCGGCAGA
AGATCCTGGACCAGTCAGAAGCTGAGAAATCGCGCAAGGAACTCTGGGAGCTGGAGGCTCTGAGCATGGCCGTGGAGAGC
ACCGGGAACGCCAAGGCAGAGGCTGAGTCCCGTGCAGAGGCAGCCCAGATTGAGGGAGAAGGATCCGTGCTGCAGGCCAA
TCTGAAAGCAGAGGCCTTGGCCATCGAGACGGAGGCTGAGCTCCCGCGGGTACAGAAGGTCCGAGAGCTGGAACTGGTTT
ATGCCTGGGCCCAGCTGGAGCTGGAGGTGAGCAAGGCTCAGCAGCTGTCTGAGGTGGAGGTGAAGAAGTTCAAGCAGATG
ACAGAGGCTCTGGGCCCCAGCACCATCAGGGACCTTGCTATGGCTGGGCCTGAGATGCAGGTCAAACTGCTCCAGTCCCT
GGGCCTGAAATCAACCCTGATCACTGATGGTTCCACTCCCATCAATCTCTTCAACACGGCTTTGGGCTGCTGGGGATGGG
GCCTGAGGGTCAGCCCCTGGGCAAAGGGTGGTCAGTGGGCCCAGCCCCGGGGAGGGCATATCCCTTCAGTCTGCTCAGAC
CCCCAAAGCTCCTGCAGACAACCACGTGGTGCCTGTACTGCAC

Alignment

ORF - retro_cjac_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.88 %
• Parental protein coverage: 64.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GIQDVYVLSEQEGLLLRALQPLEEGEDVEKVSRQAGDHWLIRGPLEYVPSAKVEVVEERQAIPLDENEGI
          GIQDVY.LSEQEGLLLRALQPLE.GEDVEKVSRQAGDHWLIRG.LEYVPSAKVEVVEERQAIPLDENEGI
Retrocopy GIQDVYMLSEQEGLLLRALQPLEDGEDVEKVSRQAGDHWLIRGLLEYVPSAKVEVVEERQAIPLDENEGI

Parental  YVQDVKTGKVRAVIGSTYMLTEDEVLWEKELPPGVEELLNKGQDP-LADRGDKGTAKSLQPSAPRNKTRV
          YVQ.V.TGKV.AVIGSTYML.EDEVLWEKELPPGVEELLNKGQDP.LADRGDKGTAKSLQPS.PRNKT.V
Retrocopy YVQGVETGKVWAVIGSTYMLMEDEVLWEKELPPGVEELLNKGQDP>LADRGDKGTAKSLQPSTPRNKTHV

Parental  VSYRVPHNAAVQVYDYRAKRARVVFGPELVSLGPEEQFTVLSLSAGRPKRPHARRALCLLLGPDFFTDVI
          VSYRVPHNAAVQVYDYRAK.ARVVFGPELVSLGPEE.F.VLSLSAG.PK.PHA.RALCLLLGPDFFTDV.
Retrocopy VSYRVPHNAAVQVYDYRAK*ARVVFGPELVSLGPEEHFMVLSLSAGWPKCPHAHRALCLLLGPDFFTDVT

Parental  TIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIASRVRGAVA-SVAFDDFHKNSA
          TIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIAS.VRG.......FDDFHKNSA
Retrocopy TIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIASWVRGGCG<PLTFDDFHKNSA

Parental  RIIRTAVFGFETSEAKGPDGIALPRPRDRAVFPQNGLVVSSVDVQSVEPVDQRTQDALQRSVQLAIEITT
          RIIRTAVFGFETSEAKGPDGI.LPRPRDRAVF.QNGLVV.S.DV.SVEPVDQRT.DALQRSV.LAIEITT
Retrocopy RIIRTAVFGFETSEAKGPDGITLPRPRDRAVFSQNGLVVRSMDV*SVEPVDQRTRDALQRSV*LAIEITT

Parental  NSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEALSMAVESTGNAKAEAESRAEAARIE
          NSQEAA.KHEAQRLEQEAR.RLERQKILDQSEAEK.RKEL.ELEALSMAVESTGNAKAEAESRAEAA.IE
Retrocopy NSQEAATKHEAQRLEQEARSRLERQKILDQSEAEKSRKELWELEALSMAVESTGNAKAEAESRAEAAQIE

Parental  GEGSVLQAKLKAEALAIETEAELQRVRKVRELELVYARAQLELEVSKAQQLAEVEVKKFKQMTEALGPST
          GEGSVLQA.LKAEALAIETEAEL.RV.KVRELELVYA.AQLELEVSKAQQL.EVEVKKFKQMTEALGPST
Retrocopy GEGSVLQANLKAEALAIETEAELPRVQKVRELELVYAWAQLELEVSKAQQLSEVEVKKFKQMTEALGPST

Parental  IRDLAVAGPEMQVKLLQSLGLKSTLITDGSTPINLFNTA-FGLLGMGPEGQPLGR-RVVSGPSPGEGISL
          IRDLA.AGPEMQVKLLQSLGLKSTLITDGSTPINLFNTA.FGLLGMGPEGQPLG..RVVSGPSPGEGISL
Retrocopy IRDLAMAGPEMQVKLLQSLGLKSTLITDGSTPINLFNTA<FGLLGMGPEGQPLGK<RVVSGPSPGEGISL

Parental  QSAQAPKAPADNHVVPVLH
          QSAQ.PKAPADNHVVPVLH
Retrocopy QSAQTPKAPADNHVVPVLH

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	193.65 RPM
SRP051959_heart	0.00 RPM	22.00 RPM
SRP051959_kidney	0.11 RPM	54.27 RPM
SRP051959_liver	0.02 RPM	17.42 RPM
SRP051959_lung	0.00 RPM	34.83 RPM
SRP051959_lymph_node	0.09 RPM	43.35 RPM
SRP051959_skeletal_muscle	0.07 RPM	18.45 RPM
SRP051959_spleen	0.04 RPM	37.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_444 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_444 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_444 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	ENSCJAG00000007166	1 retrocopy	retro_cjac_444 ,