RetrogeneDB ID: retro_cjac_1091

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:39219184..39220230(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011044
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GNAI2
• Ensembl ID: ENSCJAG00000004925
• Aliases: None
• Description: None

Sequence

>retro_cjac_1091
ATGGGGTGCACCGTGAGCATCGAGGACAAGATGGTGGCTGAGTGCTCTAAGATGATCAACAAGACCTGCGAGAAGGCGGC
GCGGGAGGTGAAGTTGCTGCTGTTGGGTGCTGGGGAGTCAGGGAAGAGCACCATCGTCAAGCAGATGATCATCCAGGAGG
ATGGCTACTCCGAGGAGGAATGCCGGCAGTACAGGGCGGTTGTCTACAGCAACACTGTCCAGTCCATCATGGCCATTGTC
AAGGCCATGGGCAACCTGCAGATCGATTTCGCCGACCCCTGCAGAGCGGATGATGCCAGGCAGCTGTTTGCACTGTCCTG
CACTGCTGAGGAGCAGGGCGTGCTCCCTGATGACCTGTCCGGTGTCATCCGGAGGCTCTGGGCTGACCATGGTGTGCAGG
CCTGCTTTGGCCACTTGGGGGAATACCTGCTTAACGACTCAACCGCCTACTACCTGAATGACCGGGAGTGCATTGCACAG
AGTGACTACATGCCCACACAGCAAGATGTGCTAGGACCCACGTAAAGACCACAGGGATCGTGGAGACACACTTCACCTTC
AAGGACTTACACTTCAAGATATTTGATGTGGGTGGTCAGCGGTCTGAGCAAAAGAAGTGAATCCACTGCTTTGAGGGTGG
CACAGCCATCCTCTTCTGCATAGCATTGAGCTCCTATGACTTGGTGCTAGCTGAGGACGAGGAGATGAACTGCATGCATG
AGAGCATGAAGCTATTCGACAGCATCTGCAACAAGTGGTCCACAGACATGTCCATCATCCTCTTCCTCAACAAGAAGGAT
CTATTCAAGGAGAAGATCACACACAGTCCCCTGGTCATCTGCTTCCCTGAGTACACAGGGGCCAACAAGTATGATGAGGC
AGCCAGCCACATCCAGAGTAAGTTTGAGGACCTGAATAAGCGCAAAGATACCAAGGAGATCTACACGCACTTCACGTGTG
CCACCAACACCAAGAACGTGCACTTTGTGTTTGACGCCATCACTGATGTCATTATCAAGAACAACCTGAAGGACTGCAGC
CTCTTC

Alignment

ORF - retro_cjac_1091 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.2 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEDGYSEEECRQYR
          MGCTVS.EDK..AE.SKMI.K......EKAAREVKLLLLGAGESGKSTIVKQM.II.EDGYSEEECRQYR
Retrocopy MGCTVSIEDKMVAECSKMINKTC----EKAAREVKLLLLGAGESGKSTIVKQM-IIQEDGYSEEECRQYR

Parental  AVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVLPDDLSGVIRRLWADHGVQAC
          AVVYSNT.QSIMAIVKAMGNLQIDFADP.RADDARQLFALSCTAEEQGVLPDDLSGVIRRLWADHGVQAC
Retrocopy AVVYSNTVQSIMAIVKAMGNLQIDFADPCRADDARQLFALSCTAEEQGVLPDDLSGVIRRLWADHGVQAC

Parental  FGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVL-RTRVKTTGIVETHFTFKDLHFKMFDVGGQRSER
          FG...EY.LNDS.AYYLND.E.IAQSDY.PTQQDVL.RT.VKTTGIVETHFTFKDLHFK.FDVGGQRSE.
Retrocopy FGHLGEYLLNDSTAYYLNDRECIAQSDYMPTQQDVL<RTHVKTTGIVETHFTFKDLHFKIFDVGGQRSEQ

Parental  KKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKI
          KK.IHCFEG.TAI.FC.ALS.YDLVLAEDEEMN.MHESMKLFDSIC.NKW.TD.SIILFLNKKDLF.EKI
Retrocopy KK*IHCFEGGTAILFCIALSSYDLVLAEDEEMNCMHESMKLFDSIC-NKWSTDMSIILFLNKKDLFKEKI

Parental  THSPLVICFPEYTGANKYDEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNL
          THSPLVICFPEYTGANKYDEAAS.IQSKFEDLNKRKDTKEIYTHFTCAT.TKNV.FVFDA.TDVIIKNNL
Retrocopy THSPLVICFPEYTGANKYDEAASHIQSKFEDLNKRKDTKEIYTHFTCATNTKNVHFVFDAITDVIIKNNL

Parental  KDCGLF
          KDC.LF
Retrocopy KDCSLF

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	0.02 RPM	35.54 RPM
SRP051959_heart	0.00 RPM	40.31 RPM
SRP051959_kidney	0.07 RPM	25.78 RPM
SRP051959_liver	0.02 RPM	24.24 RPM
SRP051959_lung	0.11 RPM	78.08 RPM
SRP051959_lymph_node	0.02 RPM	81.78 RPM
SRP051959_skeletal_muscle	0.02 RPM	19.37 RPM
SRP051959_spleen	0.06 RPM	72.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1091 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1091 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1091 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000005305	1 retrocopy	retro_cint_14,
Callithrix jacchus	ENSCJAG00000004925	1 retrocopy	retro_cjac_1091 ,
Ciona savignyi	ENSCSAVG00000001800	1 retrocopy	retro_csav_19,
Felis catus	ENSFCAG00000007008	1 retrocopy	retro_fcat_157,
Otolemur garnettii	ENSOGAG00000012525	1 retrocopy	retro_ogar_1470,
Rattus norvegicus	ENSRNOG00000016592	1 retrocopy	retro_rnor_505,