RetrogeneDB ID: retro_cjac_1136

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38429866..38430700(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPDYC
• Ensembl ID: ENSCJAG00000002403
• Aliases: None
• Description: speedy/RINGO cell cycle regulator family member C [Source:HGNC Symbol;Acc:32681]

Sequence

>retro_cjac_1136
TTAATGTTCCAGAGAAGGGATTCCCAAGACCCCACCACTTCCCCTGTAGTTACCACCCAGGTAGAGCTGGGGGGCTGCAG
CCGGCAAGGTGGAGGAAATGGGTTCCTCCATTTCGCCAGCACGAAGAGCTCCAGGCCTTCCTCAACCTTCTGGAGGACAG
TTTTGTCCAGGAATTCCTCTCCAAAGACCCCTGCTTCCAGATTTCACGTAAGTATCTCCTGGCCATGGTGCTGGTCTACT
TCCAGCGCGCCCACCTGAAGCTCAGCGAGTGCACCCACAGCAGCCTGTTCTTGGCCCTGTACCTTGCAAATGACATGGAG
GAGGACCTGGAGGGGCCCAAATGTGAGATTTTTCCATGGGCCCTGGGAAGAGATTGGCGTTTATGAGGGGGGAAGTTCCT
GCAGCAGAGGGATAAGCTGTGGGCACGGATGGATTTCCGAGCTGTCGTGAGCCGCCAGTGTTGTGAGGAGGTCATGGCAA
AGGAGCCATTCCACTGGGCTTGGACTCGGGACCGGTGCCCCTACCATGGCAGGGTTCAGAGGGTCTGTCCACAGGTCCCT
TTCCGCCTTCCCCGGGGCCCTGGCCTCTTGCCACTCCACTGTTCCCCCGTGGCTTGCCCCAGCACCGCAGCTGCCACCCA
CTTAAGCCTGTGTCATTCAAGTGCTCTTCTCTGACCTCGGAGTGTCATTGCCTTCCCTTCCAAAATTCTCTCTCAGCATT
CAAAAACGCCTGGGGCTGGGACTTTCTCCTCATCTTACCCCCTCCCAGATGCAACTGGAACCTGACACCTACTGCCTCCG
CCTTTTCCCAAAGCTTCTGCCATGCCCTGGGCAC

Alignment

ORF - retro_cjac_1136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.82 %
• Parental protein coverage: 94.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ISYEMDDSQDPTTSAVVMTQVELEGCSQQGGGNGFLSF-RQHEELQAFLNLLEDSFVQEFLSKDPCFRIS
          ......DSQDPTTS.VV.TQVEL.GCS.QGGGNGFL.F.RQHEELQAFLNLLEDSFVQEFLSKDPCF.IS
Retrocopy LMFQRRDSQDPTTSPVVTTQVELGGCSRQGGGNGFLHF<RQHEELQAFLNLLEDSFVQEFLSKDPCFQIS

Parental  DKYLLAMVLVYFQRARLKLSEYTHSSLFLALYLANDMEEDLEGPKCQIFPWALGRDWCLRVGKFLQQRDK
          .KYLLAMVLVYFQRA.LKLSE.THSSLFLALYLANDMEEDLEGPKC.IFPWALGRDW.L..GKFLQQRDK
Retrocopy RKYLLAMVLVYFQRAHLKLSECTHSSLFLALYLANDMEEDLEGPKCEIFPWALGRDWRL*GGKFLQQRDK

Parental  LWARMGFRAVVSRQCCEEVMAKEPFHWAWTRDRRPHHGGVQRVCPQVPFRLPRGPGLSPPHCSPC-GLPQ
          LWARM.FRAVVSRQCCEEVMAKEPFHWAWTRDR.P.HG.VQRVCPQVPFRLPRGPGL.P.HCSP..GLPQ
Retrocopy LWARMDFRAVVSRQCCEEVMAKEPFHWAWTRDRCPYHGRVQRVCPQVPFRLPRGPGLLPLHCSPV<GLPQ

Parental  HPGCHPLKPVSLKCSSLTSECHRLPSQNSLSAFKNTWGGDFLLIL-PP-QIQLEPDTYCLRIFPKLLPRP
          H..CHPLKPVS.KCSSLTSECH.LP.QNSLSAFKN.WG.DFLLIL.PP.Q.QLEPDTYCLR.FPKLLP.P
Retrocopy HRSCHPLKPVSFKCSSLTSECHCLPFQNSLSAFKNAWGWDFLLILPPP<QMQLEPDTYCLRLFPKLLPCP

Parental  GH
          GH
Retrocopy GH

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	0.38 RPM
SRP051959_heart	0.00 RPM	0.61 RPM
SRP051959_kidney	0.02 RPM	0.40 RPM
SRP051959_liver	0.00 RPM	0.61 RPM
SRP051959_lung	0.00 RPM	0.98 RPM
SRP051959_lymph_node	0.00 RPM	0.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.37 RPM
SRP051959_spleen	0.00 RPM	0.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1136 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1136 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002403	2 retrocopies	retro_cjac_1136 , retro_cjac_1851,
Monodelphis domestica	ENSMODG00000010068	3 retrocopies	retro_mdom_1043, retro_mdom_1348, retro_mdom_1695,
Otolemur garnettii	ENSOGAG00000015020	1 retrocopy	retro_ogar_2812,