RetrogeneDB ID: retro_cjac_4229

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: Y:246193..247133(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDYL
• Ensembl ID: ENSCJAG00000021374
• Aliases: None
• Description: None

Sequence

>retro_cjac_4229
GGAGCAGTACCATTTACCGAATTGTTAACAGCAAATCGAAAAACAAACACCAATATCTGTTCAACCATGAGAGATAAAAA
GAGAAAAGTCGTAGATGATGGAAGAGACCAGCGTGTTTGACAAGAGAGTGCGTTTCAGCATGAGGCTGATGGAAAGTGCC
CGCACGTACAAAGACATTGCGGTGAGAAAGAAAGAAGGTTTCACTCAGATCTTACTATCAACCAGATCAACACATAATAA
CACCTTGAACAGAGAGGTAATGAATGAAATTCAGAGTGCTCTGGATAGAGCTGCTGTTGATGACAGTAAGTTTGTGCTGC
TCAGTGCAGTTGGCAGTGTCTTTTGCTGTGGTCTTGATTTCGATAACTTTGTGAAGCATTTAAAATATAATAGAAAAAGA
GCTAGTGTTAAACTAGTGGACACCATCAAAAACTTTGTGAATTCTTTTATTGAGTTTCAGAAACCTATCATCGTATCAGT
CAATGGCCCAGCCATTGGACTAGGTGCATCTATACTGCCTCTCTGTGATGTGGTTTGGGCTAATGAGAAGGCTTGGTTTC
AAACCCCTTACACAAGGTTTGGGCAGAGTCCAGATGGCTGTTCCACAATTACTTTTCCAAAAATAATGGGTAGAGCAGCT
GCCAACGAAATGTTGATCAATGGGTGGAAGATGAATGCCCAAGAAGCATGTGCCAAAGGCCTCGTCTCTCAGGTGTTTTG
GCCTGAAACTTTCACACAAGAAGTTATGGTTCGAATTCAGGAGATTGCTTCATGCAATTCATTTGTTCTGGAGAATTCCA
AAGCTCTTGTGCACCATAACATGAAGATAGAGTTGAAACAGGCCAATGAGAGAGAGTGTGAAGTCCTGAAGGAAATCTGG
GGATCAGCAAAAGGAATGGAATATATGATGAACTATGTGCGAAATAAAATTGATACGTTT

Alignment

ORF - retro_cjac_4229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.16 %
• Parental protein coverage: 57.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTSPFMDALTANGTTNIQTSVTGVTTSKRKFIDDRRDQP-FDKRLRFSVRQTESAYRYRDIVVRKQDGFT
          G..PF...LTAN..TN.....T.....KRK..DD.RDQ..FDKR.RFS.R..ESA..Y.DI.VRK..GFT
Retrocopy GAVPFTELLTANRKTNTNICST-MRDKKRKVVDDGRDQR>FDKRVRFSMRLMESARTYKDIAVRKKEGFT

Parental  HILLSTKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKM
          .ILLST.S..NN.LN.EVM.E.QSAL..AA.DDSK.VLLSAVGSVFCCGLDF..F...L...RKR.S.K.
Retrocopy QILLSTRSTHNNTLNREVMNEIQSALDRAAVDDSKFVLLSAVGSVFCCGLDFDNFVKHLKYNRKRASVKL

Parental  AEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTIMFPKI
          ...I.NFVN.FI.F.KPIIV.VNGPAIGLGASILPLCDVVWANEKAWFQTPYT.FGQSPDGCSTI.FPKI
Retrocopy VDTIKNFVNSFIEFQKPIIVSVNGPAIGLGASILPLCDVVWANEKAWFQTPYTRFGQSPDGCSTITFPKI

Parental  MGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMRLEL
          MG.A.ANEML..G.K..AQEAC.KGLVSQVFWP.TFTQEVMVRI.E.ASCN..VLE.SKALV..NM..EL
Retrocopy MGRAAANEMLINGWKMNAQEACAKGLVSQVFWPETFTQEVMVRIQEIASCNSFVLENSKALVHHNMKIEL

Parental  EQANERECEVLKKIWGSAQGMDSMLKYLQRKIDEF
          .QANERECEVLK.IWGSA.GM..M..Y...KID.F
Retrocopy KQANERECEVLKEIWGSAKGMEYMMNYVRNKIDTF

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	10.98 RPM
SRP051959_heart	0.02 RPM	9.65 RPM
SRP051959_kidney	0.02 RPM	10.18 RPM
SRP051959_liver	0.00 RPM	4.74 RPM
SRP051959_lung	0.02 RPM	12.27 RPM
SRP051959_lymph_node	0.02 RPM	10.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.22 RPM
SRP051959_spleen	0.00 RPM	11.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4229 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4229 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011787	1 retrocopy	retro_chof_525,
Callithrix jacchus	ENSCJAG00000005695	1 retrocopy	retro_cjac_93,
Callithrix jacchus	ENSCJAG00000021374	5 retrocopies	retro_cjac_2675, retro_cjac_3927, retro_cjac_4003, retro_cjac_4228, retro_cjac_4229 ,
Homo sapiens	ENSG00000153046	1 retrocopy	retro_hsap_4651,
Otolemur garnettii	ENSOGAG00000015920	2 retrocopies	retro_ogar_2406, retro_ogar_3269,
Pan troglodytes	ENSPTRG00000017688	1 retrocopy	retro_ptro_3090,