RetrogeneDB ID: retro_cjac_2838

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:109579794..109580503(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCCIP
• Ensembl ID: ENSCJAG00000012411
• Aliases: None
• Description: BRCA2 and CDKN1A interacting protein [Source:HGNC Symbol;Acc:978]

Sequence

>retro_cjac_2838
CAGCAGCCTTTTCTAAAGGCTCCTGTGAACACTGCAGAGCTAACAGATGTCTTAATTCAACAGAACCATATTGGGAGTGT
GATTAAGCAAACTAATGTTTCAGAAGACAGCGATGATGATGTGGATGAAGATGAGATTTTTGGTTTCATAAGCCTTTTGA
ATTTAACTGAAAGAAAGGGTACTCAGTGTGCTGAACAAATTAGAGAGTTGATTCTAAGCTTCTGTGAGAAGAACTGTGAA
AAGAGCATGGTTGAACATTTGGACATGCTTTTAAATGACACCACCAAGCCTGTGGGCCTTCTCCTAAGTGAAAGATTCAT
TAAGGTCCCTCCACAGATCGCTCTGCCCGTGTACCAGCAGCTTCAGAAAGAAGTAGTGGAGGCACACAAAACCAATAAGC
CATGTGGGAAGTGCTGCTTTTACTTTCTGATTAGTAAGACATTTGTGGAAGCAGGAAAAAAAAAATTCCAGAAAGAAATG
GAGCAACCAAAAGAAAGATGAGTTAATGTTTGCAAATGCAGAGGAAGAATTTTTCTATGAGAAGGCAATTCTGAAGTTCA
GCTACTCAGTGCAGGAGGAGAGCGACACCTGTCTGGGTGGCAGATGGTCTTTTGATGACGTACCAATGAAGCCTTTGTGA
ATTGTGATGTTAATTCCAGGTGACAAGATGAACGAAATCATGGATAAACTGAAAGAATATCTATCTGTC

Alignment

ORF - retro_cjac_2838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.51 %
• Parental protein coverage: 75.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QQLFLKAPVNTAELTDVLIQQNHIGSVIKQTNVSEDSDDDVDEDEIFGFISLLNLTERKGTQCAEQIKEL
          QQ.FLKAPVNTAELTDVLIQQNHIGSVIKQTNVSEDSDDDVDEDEIFGFISLLNLTERKGTQCAEQI.EL
Retrocopy QQPFLKAPVNTAELTDVLIQQNHIGSVIKQTNVSEDSDDDVDEDEIFGFISLLNLTERKGTQCAEQIREL

Parental  ILSFCEKNCEKSMVEQLDKLLNDTTKAVGLLLSERFINVPPQIALPMYQQLQKEVVEAHKTNKPCGKCCF
          ILSFCEKNCEKSMVE.LD.LLNDTTK.VGLLLSERFI.VPPQIALP.YQQLQKEVVEAHKTNKPCGKCCF
Retrocopy ILSFCEKNCEKSMVEHLDMLLNDTTKPVGLLLSERFIKVPPQIALPVYQQLQKEVVEAHKTNKPCGKCCF

Parental  YLLISKTFVEAG-KNNSRKKWSNQKKDELMFANAEEEFFYEKAILKFSYSVQEESDTCLGGRWSFDDVPM
          Y.LISKTFVEAG.K.NSRKKWSNQKKDELMFANAEEEFFYEKAILKFSYSVQEESDTCLGGRWSFDDVPM
Retrocopy YFLISKTFVEAG>KKNSRKKWSNQKKDELMFANAEEEFFYEKAILKFSYSVQEESDTCLGGRWSFDDVPM

Parental  KPLRTVMLIPGNKMNEIMDKLKEYLSV
          KPL..VMLIPG.KMNEIMDKLKEYLSV
Retrocopy KPL*IVMLIPGDKMNEIMDKLKEYLSV

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	16.97 RPM
SRP051959_heart	0.09 RPM	18.79 RPM
SRP051959_kidney	0.11 RPM	23.10 RPM
SRP051959_liver	0.11 RPM	26.47 RPM
SRP051959_lung	0.23 RPM	25.41 RPM
SRP051959_lymph_node	0.18 RPM	24.02 RPM
SRP051959_skeletal_muscle	0.09 RPM	25.14 RPM
SRP051959_spleen	0.06 RPM	21.28 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2838 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2838 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012873	1 retrocopy	retro_cfam_1356,
Callithrix jacchus	ENSCJAG00000012411	1 retrocopy	retro_cjac_2838 ,
Dasypus novemcinctus	ENSDNOG00000002939	1 retrocopy	retro_dnov_530,
Macaca mulatta	ENSMMUG00000008541	1 retrocopy	retro_mmul_472,
Oryctolagus cuniculus	ENSOCUG00000008761	1 retrocopy	retro_ocun_843,
Otolemur garnettii	ENSOGAG00000010901	1 retrocopy	retro_ogar_1184,
Ictidomys tridecemlineatus	ENSSTOG00000011828	4 retrocopies	retro_itri_1004, retro_itri_1130, retro_itri_1513, retro_itri_559,
Tupaia belangeri	ENSTBEG00000002570	4 retrocopies	retro_tbel_1259, retro_tbel_1260, retro_tbel_2963, retro_tbel_3044,