RetrogeneDB ID: retro_cjac_4003

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL287668.1:4949..5926(+)
• 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_4003
CTCACTGCTTTCATGGCCACAGAGTCAGAGAACGAAGAAGGTATTGTGGTATTGATGTACCCTTCAACAGCCAATAAAAA
AACAAACAGGTATTCATCCGTTTCAAGAGTGAAAGCTGGAGAAAGAGAAATTACTGATGATAGAAAAGACCAGCCTTTTA
TCAAGAGGATGCATTTCACCATAAGATTAAAAGAAAGTGCCAACAGATACAGAGACATTGCAGTCAAGAAAGATGAGGGA
TTCACCCACTAATTGCTATCCACTATATCAACAGAGAAAAATAAACTAAACACAGAAGTTATTAAAGAAATCATGAATGC
TGTGGAAAGGGCTGCTGTGGATGACAGCAAGCTTGTGTTGTTCAGCGACACTGGCAGTGTCTATTGCTCTGGTCTTGATT
TTGGGTACATTGTGAAGAATTTAAGGAATGACAGAAACAGAATGAGCACTGAAATGGTGGACACCATTAAGAGCTTTGTG
AATGTTTTCATTCATTTTAGAAAACTTATCATCATATCTGTCAACGGCCCAGCCATTGGGCTAGGTGCATCCATACTACC
TCTTTGTGACTTGGTTTGAGCTAATGAAAAGGCTTATATTCAAACCCCACATATGACCTTTGGACAGAGTCCATATGGCT
GTGCTACTGCTACATTTCCAAGAATCATGGGTAAAGCAATGGCGAATGAAATGTTGATTGATGGGCGAAAGCTGACAGCA
TGGGAGGCATCTGCCAAAGGCCTCATCCCTCAGGTGTTCTTGAAATCAACTTCCATCCAAGAGGTGATGATTCAAATTAA
GAGGCTCGCTTCCTGTAATTCTGTTATACTGGAAAAGTGTAAGTCCCTTGTGTGCTGTAATATGAAGATGGAGTTGGGAC
AGGCCAATGAGAGAGAGTGTGAATGCTGAAAACAATCTGGAGCACAGCAGAAGGGATAGAACCCATGTTAAAGTATGTTC
AAACAAAAATTGATGAC

Alignment

ORF - retro_cjac_4003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.76 %
• Parental protein coverage: 60.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTAAMATGLAVNGKGTSPFMDALTANGTTNIQTSVTGVTTSKRKFIDDRRDQPFDKRLRFSVRQTESAYR
          .TA.MAT....N..G....M...TAN..TN...SV..V....R...DDR.DQPF.KR..F..R..ESA.R
Retrocopy LTAFMATE-SENEEGIVVLMYPSTANKKTNRYSSVSRVKAGEREITDDRKDQPFIKRMHFTIRLKESANR

Parental  YRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDFIYFIR
          YRDI.V.K..GFTH.LLST.S.E.N.LN.EV..E...A...AA.DDSKLVL.S..GSV.C.GLDF.Y...
Retrocopy YRDIAVKKDEGFTH*LLSTISTEKNKLNTEVIKEIMNAVERAAVDDSKLVLFSDTGSVYCSGLDFGYIVK

Parental  RLTDDRKRESTKMAEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQ
          .L..DR.R.ST.M...I..FVN.FI.F.K.II..VNGPAIGLGASILPLCD.V.ANEKA..QTP..TFGQ
Retrocopy NLRNDRNRMSTEMVDTIKSFVNVFIHFRKLIIISVNGPAIGLGASILPLCDLV*ANEKAYIQTPHMTFGQ

Parental  SPDGCSTIMFPKIMGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEE
          SP.GC.T..FP.IMG.A.ANEML..GRKLTA.EA..KGL..QVF...T..QEVM..IK.LASCN.V.LE.
Retrocopy SPYGCATATFPRIMGKAMANEMLIDGRKLTAWEASAKGLIPQVFLKSTSIQEVMIQIKRLASCNSVILEK

Parental  SKALVRCNMRLELEQANERECE-VLKKIWGSAQGMDSMLKYLQRKIDE
          .K.LV.CNM..EL.QANERECE..LK.IW..A.G...MLKY.Q.KID.
Retrocopy CKSLVCCNMKMELGQANERECE<MLKTIWSTAEGIEPMLKYVQTKIDD

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	0.00 RPM	9.65 RPM
SRP051959_kidney	0.00 RPM	10.18 RPM
SRP051959_liver	0.00 RPM	4.74 RPM
SRP051959_lung	0.00 RPM	12.27 RPM
SRP051959_lymph_node	0.00 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_4003 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4003 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,