RetrogeneDB ID: retro_cjac_3189

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:19884283..19885498(+)
• Located in intron of: ENSCJAG00000005332

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF38B
• Ensembl ID: ENSCJAG00000002510
• Aliases: None
• Description: PRP38 pre-mRNA processing factor 38 (yeast) domain containing B [Source:HGNC Symbol;Acc:25512]

Sequence

>retro_cjac_3189
TTATCCTCAACCTGAAAGCAAGTGATGGGTCTTATAACACACACAGACCCTCCATATATTAGAGCACTTGGATTGATGTA
TATAAGATATACACAGCCCACTACAGATCTATGGGACTGGTTTGAATCCTTCCTTGATGATGAAGAGGACCTAGAAGTGA
AGGCTGGTGGAGGCTGTGTGATGACCATTGGAGAAATGCTACCATCTTTTCTCACAAAACTGGAACGGTTTTCTACCTTG
TTTCCAAGAATTCCAGTTCCAGTTCAAAAGAATATTGATCAACAGATTAAAACCCGACCTAGAAAAATTAAGAAAGAAGG
GAAGGAAGGCGTTGAGGAAATAGACAGACATGTTAAACGCAGAAGTTCAAGGTCTCCAAGGAGATCTCTGAGTCCACGGA
GGTCCCCAAGAAGATCAAGAAGTAGAAGTCATCATTGAGAGGGCCATGGGTCTTCTAGTTTTGACAGAGCATTAGAAAGA
ATTTGACAGAGAAAGAACGTCAGCGACTAGAGCGTGAAGCCAAAGAAAGGGAGAAAGAACGCCGAAGATCTCGAGGTATT
GATCGGGGGTTAGAACAGCAGAAGCAGAAAAAGGCACAGAAGTCGCAGCCGGAGTCATGATAGGAAAGGGGATAGAAGGG
ACAGGGATCGGGAAAGAGAAAAAGAAAGTGAGAGAGGTAGAAGACGAGATCGTGACTATGATAAGGAAAGAGGAAACGAC
CGAGAAAGAGAGAGCGATCAAGAGAACTGTCCACGGAACAGAGAAGTAGGGGAGAGGTAGAAGACAAGAAACATAAAGAA
GACAAAGATGACAGGCGGCACAGAGACGACAAAAAAGATTCCAAGAAAGAAAAAACACAGGAGAAGCAGAAGCAGAGAAA
GGAAACACAGAAGTAGGAGTCGAAGTAGAAATGCAGGGAAACGAAGTAGTAGAAGCAAAAAGAAATGAAGTAAACATAAA
AATGAAAGTAAAGAAAAATCAAATAAACGAAGTAGAAGTGGCAGTCAAGGAAGAACTGACAGTCTCGAAAAATCAAAACC
ATGGGAACATAGCCCCAGCAAAGAAAAATCTACAAAGCGCAGTGGAAGCAAAGAACGTTCCCACAAACGAGATCACAGTG
ATAGTAAGGACCAGTCAGACAAACATGATCGTCGAAGGAGCCAAAGTATAGAACGAGAGAGCCAAGAAAAACAACACAAA
AACGAAGAGGAGACT

Alignment

ORF - retro_cjac_3189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.15 %
• Parental protein coverage: 74.73 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LKLTRKQVMGLITHTDSPYIRALGFMYIRYTQPPTDLWDWFESFLDDEEDLDVKAGGGCVMTIGEMLRSF
          L..T.KQVMGLITHTD.PYIRALG.MYIRYTQP.TDLWDWFESFLDDEEDL.VKAGGGCVMTIGEML.SF
Retrocopy LSST*KQVMGLITHTDPPYIRALGLMYIRYTQPTTDLWDWFESFLDDEEDLEVKAGGGCVMTIGEMLPSF

Parental  LTKLEWFSTLFPRIPVPVQKNIDQQIKTRPRKIKKEGKEGIEEIDRHVERRRSRSPRRSLSPRRSPRRSR
          LTKLE.FSTLFPRIPVPVQKNIDQQIKTRPRKIKKEGKEG.EEIDRHV.RR.SRSPRRSLSPRRSPRRSR
Retrocopy LTKLERFSTLFPRIPVPVQKNIDQQIKTRPRKIKKEGKEGVEEIDRHVKRRSSRSPRRSLSPRRSPRRSR

Parental  SRSHHREGHGSSSFDRELEREKERQRL-EREAKE-REKE--RRRSRSIDRGLERRHSRSRERHRSRSRSR
          SRSHH.EGHGSSSFDR.LER...R.....R...E..E.E..RRRSR.IDRGLE...........S...S.
Retrocopy SRSHH*EGHGSSSFDRALERI*QRKNV<QRLEREAKEREKERRRSRGIDRGLEQQ--KQKKAQKSQPES*

Parental  DRKGDRRDRDREREKENER-GRRRDRDYDKERGNDREKERERSR-ERSKE-QRSRGEVEEKKHKEDKDDR
          ...G........R....ER..RR.DRDYDKERGNDRE.E.......R..E..R...E....K...D..DR
Retrocopy *ERG*KGQGSGKRKRK*ER>RRR-DRDYDKERGNDRERESDQENCPRNRE<SRGEVEDKKHKEDKD--DR

Parental  RHRDDKKDSKKEKKHSRSRSRERKHRSRSR-SRNAGKRSRSRSKEKSSKHKNESKEKSNKRSRSGSQGRT
          RHRDDKKDSKKEK.......R.......S.........SRS....K.SKHKNESKEKSNKRSRSGSQGRT
Retrocopy RHRDDKKDSKKEKTQEKQKQRKETQK*ESK>RNAGKRSSRSK--KK*SKHKNESKEKSNKRSRSGSQGRT

Parental  DSLEKSKKWEHSPSKEKSRKRSGSKERSHKRDHSDSKDQSDKHDRRRSQSIEQESQEKQHKNKEET
          DSLEKSK.WEHSPSKEKS.KRSGSKERSHKRDHSDSKDQSDKHDRRRSQSIE.ESQEKQHKN.EET
Retrocopy DSLEKSKPWEHSPSKEKSTKRSGSKERSHKRDHSDSKDQSDKHDRRRSQSIERESQEKQHKNEEET

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	0.24 RPM	18.84 RPM
SRP051959_heart	0.37 RPM	24.31 RPM
SRP051959_kidney	0.20 RPM	29.62 RPM
SRP051959_liver	0.39 RPM	20.60 RPM
SRP051959_lung	0.36 RPM	39.04 RPM
SRP051959_lymph_node	0.27 RPM	47.92 RPM
SRP051959_skeletal_muscle	0.09 RPM	19.22 RPM
SRP051959_spleen	1.83 RPM	39.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3189 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3189 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3189 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002510	1 retrocopy	retro_cjac_3189 ,
Nomascus leucogenys	ENSNLEG00000001645	1 retrocopy	retro_nleu_350,
Tursiops truncatus	ENSTTRG00000006479	1 retrocopy	retro_ttru_236,