RetrogeneDB ID: retro_cjac_2528

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:65562574..65563815(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTBP2
• Ensembl ID: ENSCJAG00000012539
• Aliases: None
• Description: C-terminal binding protein 2 [Source:HGNC Symbol;Acc:2495]

Sequence

>retro_cjac_2528
ATGGCCCTTGTGGATAAGCACAAAGTCAAGAGACAGCGATTGGACAGAATTTGTAAAGGTATCCGCCCCCAGATCATGAA
CGGGCCCGCTGCACCCCCGCCCCCTGGTGGCGCTGCTGGACGGCCGCGACTGCACCGTGGAGATGCCCATCCTGAAGGAC
CTGGCCACTGTGGCCTTCTGTGACGCGCAGTCCACTTAGGAGATCCACGAGAAGGTTCTAAATGAAGTCGTGGGTGCCAT
GATGTACCACACCATCACCCTCACCAGGGAAGACCTAGAAAAGTTCAGGCTCTGAGAGTGATCTGCGGATAGGCAGCGGC
TATGACAACGTGGACATCAAGGCTGCCTGCAAGCTGGGAATCGCTGTGTGCAACATCCCGTCCGAAGCCATGGAAGAGAC
GGCTGACTCCACCATCTGCCACATCCTCAATCTGTACCGGAGGAACACGTGGCTGTACCAGGCCCTTCGGGAAGGCACGC
GGGTTCTGAGCCTGGAGCAGGTCTGCGAGGTGGCCTTGGGAGCGGCCCGTAACCGTGGAGAGACACGGGGCCTCATCGGC
TTTGGTCGCACGGGGCAGGCGGTTGCAGTTCGATCCAAGGCCTTTGGATTCAGCGTCATATTTTATGACCCCTACTTGCA
GGATGGGATCTAGCGGTCCCTGGGCGTGCAGACGGTCTACACGCTGCAGGATTTGCTGTATCAGAGCGACTGCGTCTCCC
TGCACTGCAATCTCAACGAACATAACCACCAGCTCATCAAGGACCTTACCATAAAGCAGATGAGGCAGGGAGCATTCCTT
GTGAACGCAGCCCATGGGGGCCTGATGGACGAGAAAGCCTTAGCACAGGCCCTCAAGGAGGGCAGGATACGAGGGGCAGC
CCACGATGTGCATGAGTCGGAGCCCTTCAGCTTTGCTCAGGGTCCGTTGAAAGATGCACGGAATCTCATCTGCACTCCTC
ACACTGCCTGGTACAGCCAGCAGGCGTCGCTGGAAATGAGGGAGGCGGCTGCCACCGAGATCCGCAGAGCCATCACAGGT
CGCATCCCAGAGAGCTTAAGAAACTGTGTGAACAAGGAATTTTTCGTCACATCAGCGCCTTGGTCAGTAATAGACCAGCA
AGCAATTCATCCTGAGCTCAATGGTGCCACATACAGATACCCGCCAGGCATCGTGGGCGTGGCTCCAGGCGGACTTCCTG
CAGCCATGGAAGGGATCATCCCTGGGGGCATCCCAGTGACT

Alignment

ORF - retro_cjac_2528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.81 %
• Parental protein coverage: 93.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALVDKHKVKRQRLDRICEGIRPQIMNGP-LHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIH
          MALVDKHKVKRQRLDRIC.GIRPQIMNGP.LHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQST.EIH
Retrocopy MALVDKHKVKRQRLDRICKGIRPQIMNGP>LHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQST*EIH

Parental  EKVLNEAVGAMMYHTITLTREDLEKFK-ALRVI-VRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADS
          EKVLNE.VGAMMYHTITLTREDLEKF..ALRVI..RIGSGYDNVDIKAA..LGIAVCNIPS.A.EETADS
Retrocopy EKVLNEVVGAMMYHTITLTREDLEKFR<ALRVI<LRIGSGYDNVDIKAACKLGIAVCNIPSEAMEETADS

Parental  TICHILNLYRRNTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVI
          TICHILNLYRRNTWLYQALREGTRV.S.EQ..EVA.GAAR.RGET.GLIGFGRTGQAVAVR.KAFGFSVI
Retrocopy TICHILNLYRRNTWLYQALREGTRVLSLEQVCEVALGAARNRGETRGLIGFGRTGQAVAVRSKAFGFSVI

Parental  FYDPYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAARGGLVD
          FYDPYLQDGI.RSLGVQ.VYTLQDLLYQSDCVSLHCNLNEHNH.LI.D.TIKQMRQGAFLVNAA.GGL.D
Retrocopy FYDPYLQDGI*RSLGVQTVYTLQDLLYQSDCVSLHCNLNEHNHQLIKDLTIKQMRQGAFLVNAAHGGLMD

Parental  EKALAQALKEGRIRGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQASLEMREAAATEIRRAITG
          EKALAQALKEGRIRGAA.DVHESEPFSFAQGPLKDA.NLICTPHTAWYS.QASLEMREAAATEIRRAITG
Retrocopy EKALAQALKEGRIRGAAHDVHESEPFSFAQGPLKDARNLICTPHTAWYSQQASLEMREAAATEIRRAITG

Parental  RIPESLRNCVNKEFFVTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPAAMEGIIPGGIPVT
          RIPESLRNCVNKEFFVTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPAAMEGIIPGGIPVT
Retrocopy RIPESLRNCVNKEFFVTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPAAMEGIIPGGIPVT

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	27.78 RPM
SRP051959_heart	0.04 RPM	18.52 RPM
SRP051959_kidney	0.07 RPM	23.67 RPM
SRP051959_liver	0.00 RPM	3.70 RPM
SRP051959_lung	0.00 RPM	15.55 RPM
SRP051959_lymph_node	0.02 RPM	5.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.51 RPM
SRP051959_spleen	0.00 RPM	14.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2528 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2528 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012775	1 retrocopy	retro_cfam_1868,
Callithrix jacchus	ENSCJAG00000012539	2 retrocopies	retro_cjac_1866, retro_cjac_2528 ,
Callithrix jacchus	ENSCJAG00000019916	4 retrocopies	retro_cjac_2894, retro_cjac_2958, retro_cjac_3441, retro_cjac_3994,
Cavia porcellus	ENSCPOG00000008397	1 retrocopy	retro_cpor_1525,
Homo sapiens	ENSG00000175029	1 retrocopy	retro_hsap_403,
Oryctolagus cuniculus	ENSOCUG00000007076	1 retrocopy	retro_ocun_378,
Otolemur garnettii	ENSOGAG00000024152	2 retrocopies	retro_ogar_1393, retro_ogar_45,
Pongo abelii	ENSPPYG00000002746	10 retrocopies	retro_pabe_1706, retro_pabe_1710, retro_pabe_1711, retro_pabe_1719, retro_pabe_1737, retro_pabe_1750, retro_pabe_1773, retro_pabe_3228, retro_pabe_3230, retro_pabe_3587,