RetrogeneDB ID: retro_cjac_4228

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: Y:191268..192265(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_4228
CAGATGTCTGACTCAGTCACTGCTTCCATGGCCACAGAGTCAGATAACAAAGAAGGTATGGTGGTATTGATGGACCCTTC
AACAGCCAGTGGAAAAACAAACAGGCATACATCTGCTCCAAGAGTGAAAGCTGGAAAAAGAGAGATTATTAATGATAGAA
AAGACCAGCCTTGTATCAAGAGGATGTATTTCACCATAAGCTTAAAAGAAAGTGCCAACAGATACAGAGACATTGTTGTC
AAGAAAGACGATGGATTCACCCACATATTGCTATCCACTGTATCAATAGAGAAAAATGCACTAAACACGGAAGTTATTAA
AGAAATCATGGATGCTCTGGAAAGGGCCGCTGTGGATGACAGCAAGCTTGTGTTGTTCGGTGCAGCTGGCAGTGTCTTTT
GCTCTGGTCTTGATTTTGGGTACATTGTGAAGAATTTAAGGAATGACAGAAACAGAATGAGCATTGAAATGGTGGACACC
ATTAAGAGCTTTGTGAATGTTTTCATTCATTTTAAAAAAACTTATTGTCGTATCTGTCAATGGCCCAGCCATTGGACCAG
GTGCATCCATACTACCTCTTTGTGACTTGGTTTGGGCTAATGAAAAGGCTTGGATTCAAACCCCATATATGACCTTTGGG
CAGAGTCCAGATGGCTGTGCTACTGTTACATTTCCAAGAATCCTGGGTGAAGCATCGGCCAATGAAATGTTGATTGGTGG
GCGAAAGCTGACAGCACGGGAGGCATCTGCCAAAGGCCTGGTCTCTCAGGTGTTCTTGACTTCAACTTTCACCTGAGAGG
TGATGATTCAAATTAAGAGGCTTGCCTCCTGTAATCCTGTTATACTGGAAAAGTGTAAGGCCCTTGTGTGCTGTAATATT
AAGATGAAGTTGGAACAGGCCAATGAGAGAGAGTGTGAAATGCTGAAGAAAATCTGGAGCAGAGCAGAAGGGATGGAATC
CATGTTAAAATATGTTCAAACAATAATTGATGAGTTT

Alignment

ORF - retro_cjac_4228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.07 %
• Parental protein coverage: 55.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVPGPVTAAMATGLAVNGKGTSPFMDALTANGTTNIQTSVTGVTTSKRKFIDDRRDQPFDKRLRFSVRQT
          Q....VTA.MAT....N..G....MD..TA.G.TN..TS...V...KR..I.DR.DQP..KR..F.....
Retrocopy QMSDSVTASMATE-SDNKEGMVVLMDPSTASGKTNRHTSAPRVKAGKREIINDRKDQPCIKRMYFTISLK

Parental  ESAYRYRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDF
          ESA.RYRDIVV.K.DGFTHILLST.S.E.N.LN.EV..E...AL..AA.DDSKLVL..A.GSVFC.GLDF
Retrocopy ESANRYRDIVVKKDDGFTHILLSTVSIEKNALNTEVIKEIMDALERAAVDDSKLVLFGAAGSVFCSGLDF

Parental  IYFIRRLTDDRKRESTKMAEAIRNFVNTFIQFKKP-IIVAVNGPAIGLGASILPLCDVVWANEKAWFQTP
          .Y....L..DR.R.S..M...I..FVN.FI.FKK..I.V.VNGPAIG.GASILPLCD.VWANEKAW.QTP
Retrocopy GYIVKNLRNDRNRMSIEMVDTIKSFVNVFIHFKKT>IVVSVNGPAIGPGASILPLCDLVWANEKAWIQTP

Parental  YTTFGQSPDGCSTIMFPKIMGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCN
          Y.TFGQSPDGC.T..FP.I.G.ASANEML..GRKLTA.EA..KGLVSQVF...TFT.EVM..IK.LASCN
Retrocopy YMTFGQSPDGCATVTFPRILGEASANEMLIGGRKLTAREASAKGLVSQVFLTSTFT*EVMIQIKRLASCN

Parental  PVVLEESKALVRCNMRLELEQANERECEVLKKIWGSAQGMDSMLKYLQRKIDEF
          PV.LE..KALV.CN....LEQANERECE.LKKIW..A.GM.SMLKY.Q..IDEF
Retrocopy PVILEKCKALVCCNIKMKLEQANERECEMLKKIWSRAEGMESMLKYVQTIIDEF

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	0.09 RPM	9.65 RPM
SRP051959_kidney	0.00 RPM	10.18 RPM
SRP051959_liver	0.00 RPM	4.74 RPM
SRP051959_lung	0.08 RPM	12.27 RPM
SRP051959_lymph_node	0.02 RPM	10.39 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.22 RPM
SRP051959_spleen	0.06 RPM	11.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4228 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4228 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,