RetrogeneDB ID: retro_cjac_2675

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:140223345..140224275(-)
• 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_2675
CCATTTACAGATTTGTTAACAGCAAATCGAAAAACAAACACCAATATCTGTTCAACTATGAGAGGTAAAAAGAGAAAAGT
CATGGATGATGGAAGAGACCAGCGTTTTGACAAGAGGGTGCATTTCAGCGTGAGGCTGATGAAAAGTGCCAGCACATACA
AAGACATTGTGGTGAGGAAGAAAGATGGTTTCACTCAGATCTTACTATCAACCAGATCAACACATAAGAACCCCTTGAAT
AGAGAGGTAATGAATGAAATACAGAGTGCTCTGGATAGAGCGGCTGTTGATGACAGTAAGTTTGTGCTGCTCAGTGCAGT
TGGCAGTGTCTTTTGCTGTGGTCTTGATTTCGATAACTTTGTGAAGCATTTAAAATATAATAGAAAAAGAGCTAGTGTTA
AACTAGTGGACACCATCAAAAACTTTGTGAATTCTTTTATTGAGTTTCAGAAAGCTATCATCGTATCAGTCAATGGCCTA
GCCATTGGACTAGGTGCATCTATACTGCCTCTCTGTGATGTGGTTTGGGCTAATGAGAAGGCTTGGTTTCAAACCCCTTA
CACAAGGTTTGGGCAGAGTCCAGGTGGCTGTTCCACAATTACTTTTCCAAAAATAATGGGTAGAGCAGCTGCCAACGAAA
CGTTGATCAATGGGTGGAAGATACATGCCCAAGAAGCATGTGCGAAAGGCCTTGTCTCTCAGGTGTTTGGGCCTAAATCT
TTCACACAAGAAGTTATGGTTCGAATTCAGGAAATCACTTCATGCAATTCATTTGTTCTGGAGAATTCCAAAGCTCTTGT
GCGCTATAACATGAAGATAGAGTTGAAACAGGTCAATGAGAGAGAGTGTGAGGTCCTGAAGAAAATCTGGGTATCAGCAC
AAGGAATGGAATACATGTTGAAGTATGTGCAAAACAAAATTCATACGTTT

Alignment

ORF - retro_cjac_2675 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.77 %
• Parental protein coverage: 57.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PFMDALTANGTTNIQTSVTGVTTSKRKFIDDRRDQPFDKRLRFSVRQTESAYRYRDIVVRKQDGFTHILL
          PF.D.LTAN..TN.....T.....KRK..DD.RDQ.FDKR..FSVR...SA..Y.DIVVRK.DGFT.ILL
Retrocopy PFTDLLTANRKTNTNICST-MRGKKRKVMDDGRDQRFDKRVHFSVRLMKSASTYKDIVVRKKDGFTQILL

Parental  STKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKMAEAI
          ST.S...N.LN.EVM.E.QSAL..AA.DDSK.VLLSAVGSVFCCGLDF..F...L...RKR.S.K....I
Retrocopy STRSTHKNPLNREVMNEIQSALDRAAVDDSKFVLLSAVGSVFCCGLDFDNFVKHLKYNRKRASVKLVDTI

Parental  RNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTIMFPKIMGGA
          .NFVN.FI.F.K.IIV.VNG.AIGLGASILPLCDVVWANEKAWFQTPYT.FGQSP.GCSTI.FPKIMG.A
Retrocopy KNFVNSFIEFQKAIIVSVNGLAIGLGASILPLCDVVWANEKAWFQTPYTRFGQSPGGCSTITFPKIMGRA

Parental  SANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMRLELEQAN
          .ANE.L..G.K..AQEAC.KGLVSQVF.P..FTQEVMVRI.E..SCN..VLE.SKALVR.NM..EL.Q.N
Retrocopy AANETLINGWKIHAQEACAKGLVSQVFGPKSFTQEVMVRIQEITSCNSFVLENSKALVRYNMKIELKQVN

Parental  ERECEVLKKIWGSAQGMDSMLKYLQRKIDEF
          ERECEVLKKIW.SAQGM..MLKY.Q.KI..F
Retrocopy ERECEVLKKIWVSAQGMEYMLKYVQNKIHTF

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_2675 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2675 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,