RetrogeneDB ID: retro_cjac_1881

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:419979..421119(-)
• Located in intron of: ENSCJAG00000010221

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAK2
• Ensembl ID: ENSCJAG00000013687
• Aliases: None
• Description: p21 protein (Cdc42/Rac)-activated kinase 2 [Source:HGNC Symbol;Acc:8591]

Sequence

>retro_cjac_1881
GTGTCTGATAACGGAGAAATGGAAGACAAGCCTCCAGCACCTCCTGTGGGAATGAGCAGTACCATTTTTAGCACTGGAGG
CAAAGATCCTTTGTCAGCCAATCATAGTTTGAAACCTTTGCCCTCTGTTCCAGAGGAGAAAAAGCCCAGGAATAAAATCA
TCTCCATATTCTCAGGCAAAGAAACAGAAGTAAAAAGAAAGAAAAGGAATGGCCAGACATTTCTCCTCCATCTGATTTTG
AACACACTATCCATGTTGGCTTTGATGCTGTTACAGGAGAATTCACTGGCATGCCAGAACAGTGGGCTTGATTACTACAG
ACCTCCAATATCACCAAACTAGAGCAAAAGAAGAATCCTCAGGCTGTGCTGGATGTCTCAAAGTTCTACGGCTCCAACAC
AGTGAAGCAGCAAAAATATCTGAGCTTTACTCCTCCTGAGAAAAATGGCTTCCCTTCTGCAACACCACCACTGAATGCCA
AGGGACCAGAAACATCAGCAGTAGTGACAGAGGAAGATGATGATGATGATGAAGAAACCGCTCCTCCTGTTACTGCCCCA
GGACCAGATCATACAAAATCAATTTACACATGGTCTGTAATTGACCGTTTCTGCACCAGTTGGTGATTCAAACGTTGATG
GTGGTGCCAGGTCTTCAGACAAACAGAAAAAGAAGACTAAGATGACAGATGAAGAGATTATGGAGAAATTCAGAACTACT
TTGAGCATAGGTGACCCTAAGAAACAATACACAAGATATGCAAAAATTGGTCAAGGGACTTCTGGTACATTTTCACTGCT
ACTGATGCATTGGGAGAGGAGGTTGCATCAAACAGATTTACAGAAACAGCCAAAGAAGGAATTGATCATTAACGATATTC
TGGTGATGAAAGAATTAAAAAATCCCAACATATTTAACTTCTTGGACAATTACCTGGTAGGAGATTAATTGTTTGTGGTA
ATGGGAGTAACTTGCTGGTGGATCACTTACTGTCGTTGTATCAGAAACCTGTATGGATGAAGCACAGATTGCTGCTGTAT
GCAGAGAGTGTTTCAGGCACTGGGGTTTTTACATGCTAATCAAGTGATCCACAGAGACATCAAAAGTGACAATGTACTTT
TGGGAATGGAAGGATCAGTT

Alignment

ORF - retro_cjac_1881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.03 %
• Parental protein coverage: 72.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MSDNGELEDKPPAPPVRMSSTIFSTGGKDPLSANHSLKPLPSVPEEKKPRNKIISIFSGTE-KGSKKKEK
          .SDNGE.EDKPPAPPV.MSSTIFSTGGKDPLSANHSLKPLPSVPEEKKPRNKIISIFSG.E...SKKKEK
Retrocopy VSDNGEMEDKPPAPPVGMSSTIFSTGGKDPLSANHSLKPLPSVPEEKKPRNKIISIFSGKE<NRSKKKEK

Parental  ERPEISPPSDFEHTIHVGFDAVTGEFTGMPEQWARLLQTSNITKLEQKKNPQAVLDVLKFYDSNTVKQ-K
          E.P.ISPPSDFEHTIHVGFDAVTGEFTGMPEQWA.LLQTSNITKLEQKKNPQAVLDV.KFY.SNTVKQ.K
Retrocopy EWPDISPPSDFEHTIHVGFDAVTGEFTGMPEQWA*LLQTSNITKLEQKKNPQAVLDVSKFYGSNTVKQQK

Parental  YLSFTPPEKDGFPSGTPALNAKGSETSAVVTEEDDDDEETAPP-VIAPRPDHTKSIYTRSVIDPVPAPVG
          YLSFTPPEK.GFPS.TP.LNAKG.ETSAVVTEEDDDD.E...P....P.........T......V.APVG
Retrocopy YLSFTPPEKNGFPSATPPLNAKGPETSAVVTEEDDDDDEETAP>LLLPQDQIIQNQFTHGL*LTVSAPVG

Parental  DSNVDGGAKSSDKQKKKTKMTDEEIMEKLRTIVSIGDPKKKYTRYEKIGQGASGT-VFTATDVALGQEVA
          DSNVDGGA.SSDKQKKKTKMTDEEIMEK.RT..SIGDPKK.YTRY.KIGQG.SGT..FTATD.ALG.EVA
Retrocopy DSNVDGGARSSDKQKKKTKMTDEEIMEKFRTTLSIGDPKKQYTRYAKIGQGTSGT<IFTATD-ALGEEVA

Parental  -IKQINLQKQ-PKKELIINEILVMKELKNPNIVNFLDSYLVGDELFVVM-EYLAGGSLTDVVTETCMDEA
          .IKQI....Q..K...I.N.ILVMKELKNPNI.NFLD.YLVGD.LFVVM.E.LAGGSLT.VV.ETCMDEA
Retrocopy <IKQIYRNSQ<KKELII-NDILVMKELKNPNIFNFLDNYLVGD*LFVVM>E*LAGGSLTVVVSETCMDEA

Parental  QIAAVCREC-LQALEFLHANQVIHRDIKSDNVLLGMEGSV
          QIAAVCREC..QAL.FLHANQVIHRDIKSDNVLLGMEGSV
Retrocopy QIAAVCREC<FQALGFLHANQVIHRDIKSDNVLLGMEGSV

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	0.82 RPM	40.87 RPM
SRP051959_heart	0.54 RPM	36.12 RPM
SRP051959_kidney	0.42 RPM	37.65 RPM
SRP051959_liver	0.30 RPM	34.25 RPM
SRP051959_lung	0.81 RPM	61.46 RPM
SRP051959_lymph_node	0.98 RPM	71.28 RPM
SRP051959_skeletal_muscle	0.26 RPM	28.94 RPM
SRP051959_spleen	0.80 RPM	60.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1881 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1881 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1881 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	ENSCJAG00000013687	1 retrocopy	retro_cjac_1881 ,
Homo sapiens	ENSG00000180370	1 retrocopy	retro_hsap_1534,
Tursiops truncatus	ENSTTRG00000013895	1 retrocopy	retro_ttru_1360,