RetrogeneDB ID: retro_cjac_1866

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:160643527..160644862(+)
• Located in intron of: ENSCJAG00000001260

Retrocopy information

• Ensembl ID: ENSCJAG00000001266
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1866
ATGGCCCTTGTGGATAAGCACAAAGTCAAGAGACAGCGATTGGACAGAATTTGTGAAGGTATCCGCCCCCAGATCATGAA
CGGCCCCCTGCACCCCCGCCCCCTGGTGGCGCTGCTGGACGGCCGCGACTGCACTGTGGAGATGCCCATCCTGAAGCACC
TGGCCACCGTGGCCTTCTGTGACGCGCAGTCCACTCAGGAGATCCACGAGAAGGTTTTAAATGAAGCCGTGGGCGCCATG
ATGTACCACACCATCACCCTCACCAGGGAGGACCTAGAAAAGTTCAAGGCTCTGAGAGTGATCGTGCGGATAGGCAGCGG
CTACGACAATGTGGACATCAAGGCTGCCGGCGAGCTGGGAATTGCTGTGTGCAACATCCCATCCGCAGCCGTGGAAGAGA
CAGCTGACTCCACCATCTGCCACATCCTCAATCTGTACCGGAGGAACACGTGGCTGTACCAGGCCCTGCGGGAAGGCACG
CGGGTTCAGAGCGTGGAGCAGATCCGAGAGGTGGCCTCGGGAGCGGCCCGTATCCGTGGGGAGACACTGGGCCTCATCGG
CTTCGGTCGCACGGGGCAGGCGGTTGCAGTTCGAGCCAAGGCCTTTGGATTCAGCGTCATATTTTATGACCCCTACTTGC
AGGATGGGATCGAGCGGTCCCTGGGCGTGCAGAGGGTCTACACGCTGCAGGATTTGCTGTATCAGAGCGACTGCGTCTCC
CTGCACTGCAATCTCAACGAACATAACCACCACCTCATCAACGACTTTACCATAAAGCAGATGAGGCAGGGAGCATTCCT
TGTGAACGCAGCCCGTGGCGGCCTGGTGGACGAGAAAGCCTTAGCACAGGCCCTCAAGGAGGGCAGGATACGAGGGGCAG
CCCTCGACGTGCATGAGTCAGAGCCCTTCAGCTTTGCTCAGGGTCCATTGAAAGATGCACCGAATCTCATCTGCACTCCT
CACACTGCCTGGTACAGCGAGCAGGCATCGCTGGAAATGAGGGAGGCCGCTGCCACTGAGATCCGCCGAGCCATCACAGG
TCGCATCCCAGAAAACTTAAGAAACTGTGTGAACAAGGAATTTTTCGTCACATCAGCGCCTTGGTCAGTAATAGACCAGC
AAGCAATTCATCCTGAGCTCAATGGTGCCACATACAGATACCCGCCAGGCATCGTGGGTGTGGCTCCAGGCGGACTTCCT
GCAGCCATGGAAGGGATCATCCCTGGGGGCATCCCAGTGACTCACAACCTCCCGACAGTGGCACATCCTTCCCAAGCACC
CTCTCCCAACCAGCCCACAAAACACGGGGACAATCGAGAGCACCCCAACGAGCAA

Alignment

ORF - retro_cjac_1866 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALVDKHKVKRQRLDRICEGIRPQIMNGPLHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIHE
          MALVDKHKVKRQRLDRICEGIRPQIMNGPLHPRPLVALLDGRDCTVEMPILK.LATVAFCDAQSTQEIHE
Retrocopy MALVDKHKVKRQRLDRICEGIRPQIMNGPLHPRPLVALLDGRDCTVEMPILKHLATVAFCDAQSTQEIHE

Parental  KVLNEAVGAMMYHTITLTREDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTIC
          KVLNEAVGAMMYHTITLTREDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTIC
Retrocopy KVLNEAVGAMMYHTITLTREDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTIC

Parental  HILNLYRRNTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIFYD
          HILNLYRRNTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIFYD
Retrocopy HILNLYRRNTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIFYD

Parental  PYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAARGGLVDEKA
          PYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAARGGLVDEKA
Retrocopy PYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAARGGLVDEKA

Parental  LAQALKEGRIRGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQASLEMREAAATEIRRAITGRIP
          LAQALKEGRIRGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQASLEMREAAATEIRRAITGRIP
Retrocopy LAQALKEGRIRGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQASLEMREAAATEIRRAITGRIP

Parental  ESLRNCVNKEFFVTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPTV
          E.LRNCVNKEFFVTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPTV
Retrocopy ENLRNCVNKEFFVTSAPWSVIDQQAIHPELNGATYRYPPGIVGVAPGGLPAAMEGIIPGGIPVTHNLPTV

Parental  AHPSQAPSPNQPTKHGDNREHPNEQ
          AHPSQAPSPNQPTKHGDNREHPNEQ
Retrocopy AHPSQAPSPNQPTKHGDNREHPNEQ

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	0.13 RPM	27.78 RPM
SRP051959_heart	0.09 RPM	18.52 RPM
SRP051959_kidney	0.13 RPM	23.67 RPM
SRP051959_liver	0.02 RPM	3.70 RPM
SRP051959_lung	0.08 RPM	15.55 RPM
SRP051959_lymph_node	0.02 RPM	5.66 RPM
SRP051959_skeletal_muscle	0.09 RPM	12.51 RPM
SRP051959_spleen	0.08 RPM	14.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1866 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1866 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1866 has 0 orthologous retrocopies within eutheria group .

---

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,