RetrogeneDB ID: retro_cjac_3109

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:10544699..10545924(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PREP
• Ensembl ID: ENSCJAG00000001710
• Aliases: None
• Description: prolyl endopeptidase [Source:HGNC Symbol;Acc:9358]

Sequence

>retro_cjac_3109
TTTCTCAAGCAGTGTCCTATCAGCGGTTTATACAAAGAGAGAATGACTGAACTGTATGGTTATCTCAAGTATAGTTGCCA
CTTCAAGAAAGGAAAACAGTCTTTTTATTTTTACAATGCAGTTTTGCAGAACCAGCGAGTATTATATGTACAGGATTCCT
TAGAGTGTGAGGCCAAAGGATTCCTGGACCCCAAAATACTGTCTGATGATGGCATGGTGGCACTCTGAGGTTATGCGTTT
GGTGAAGATGGTGAATATTTTCCTATGGTCTGAGTGCCAGTGGCTCAGACTGGGTGATGATCAAGTTCATGAAAGATGAT
GGTGCCAAAGAGCTTCCAGATGTGCTCGAAAGAGTTAAGTTCAGCTGTATGGTCTGGACCCATGACAGGAAGAGAATGTT
CTACAACTCATACCCCCAACAGGATGGAAAAAGTGATGGTACAGAGACATCCACCAATCTCCACCAAAAGCTCTACCATC
ATGTCTTGGGAACAGATCAGTCAGAAGAGATGTTGTGTGCTGAGTTTCCTGATGAACCTAAATGGATGGGTGGAGCTGAG
TTATCAGATGATGACCGCTATATCTTGTTCTCAATAAAGGGAGGTATGTGATCCAGTAAACTGACTCTGGTACTGTGACC
TACAGCAGGAATCCAATGGCATCACTGGAATCCTAAAATGGGTAAAACTGATAGACAACTTTGAAGGAGAATATAACTAC
GTGACCAATGAGAGGATGGTGTTCATGTTCAAGGCGAATCGCCTTTCTCCCAACTATCGCATGATCAACATTGACTTCAG
GGACCCTGACGAGGCTCAGTGGAAAGTGCTTGTTCCTGAGCATGAGAAAGACGTCTTAGAAAGGGTAGCTTGTGTCAGGC
CCAACTTCGTGGTCTTATGCTACCTCCATGACATCAAGAACATTCTGCAGCTCCACAACCTGACTACTGGTGCTCTCCTC
AAGACCTTCCCGTTCCAGGTTGGCAGTGTCGTGGGGTACAGCAGTCAGAAGGACACTGAAAACTTCTATCAGTTTACTTC
CTTTTTATCTTCAGGTATCATTTATCACTGTGATCTTACCAAAGAGGAACTGGAGCCAAGAGTTTTCTGAGAGGAGGCCG
TAAAAGGAATCGATGCTTCTGATGACCAGACAGTCCAGATTTTCTACCCTAGCAAGGATGATACGAAGGTTCCAATGTTC
ACTGTGCATTAAAAAAGGCATAAAA

Alignment

ORF - retro_cjac_3109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.71 %
• Parental protein coverage: 57.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEAKVFLDPNILSDD
          FL.QCPI.GLYKERMTELY.Y.KYSCHFKKGK..FYFYN..LQNQRVLYVQDSLE.EAK.FLDP.ILSDD
Retrocopy FLKQCPISGLYKERMTELYGYLKYSCHFKKGKQSFYFYNAVLQNQRVLYVQDSLECEAKGFLDPKILSDD

Parental  GTVALRGYAFSEDGEYF-AYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYP
          G.VAL.GYAF.EDGEYF..YGLSASGSDWV.IKFMK.DGAKELPDVLERVKFSCM.WTHD.K.MFYNSYP
Retrocopy GMVAL*GYAFGEDGEYF<SYGLSASGSDWVMIKFMKDDGAKELPDVLERVKFSCMVWTHDRKRMFYNSYP

Parental  QQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAQFPDEPKWMGGAELSDDGHYVLLSI-REGCDPVNR
          QQDGKSDGTETSTNLHQKLY.HVLGTDQSE..LCA.FPDEPKWMGGAELSDD..Y.L.SI.RE.CDPVN.
Retrocopy QQDGKSDGTETSTNLHQKLYHHVLGTDQSEEMLCAEFPDEPKWMGGAELSDDDRYILFSI>REVCDPVN*

Parental  LWYCDLQQESNGITGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRHSPNYRVINIDFRDPDESKWKVLV
          LWYCDLQQESNGITGILKWVKLIDNFEGEY.YVTNE..VF.FK.NR.SPNYR.INIDFRDPDE..WKVLV
Retrocopy LWYCDLQQESNGITGILKWVKLIDNFEGEYNYVTNERMVFMFKANRLSPNYRMINIDFRDPDEAQWKVLV

Parental  PEHKKDVLEWVACVRSNFLVLCYLHDVKNILQLHDLTTGALLKSLPLEVGSVVGYSGQKKDTEIFYQFTS
          PEH.KDVLE.VACVR.NF.VLCYLHD.KNILQLH.LTTGALLK..P..VGSVVGYS.Q.KDTE.FYQFTS
Retrocopy PEHEKDVLERVACVRPNFVVLCYLHDIKNILQLHNLTTGALLKTFPFQVGSVVGYSSQ-KDTENFYQFTS

Parental  FLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVH-KKGIK
          FLS.GIIYHCDLTKEELEPRVF.E..VKGIDASD.QTVQIFYPSKD.TK.PMF.VH.KKGIK
Retrocopy FLSSGIIYHCDLTKEELEPRVF*EEAVKGIDASDDQTVQIFYPSKDDTKVPMFTVH>KKGIK

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	13.40 RPM
SRP051959_heart	0.00 RPM	17.40 RPM
SRP051959_kidney	0.00 RPM	6.37 RPM
SRP051959_liver	0.04 RPM	21.83 RPM
SRP051959_lung	0.00 RPM	10.72 RPM
SRP051959_lymph_node	0.00 RPM	12.97 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.39 RPM
SRP051959_spleen	0.00 RPM	11.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3109 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3109 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001710	1 retrocopy	retro_cjac_3109 ,
Oryctolagus cuniculus	ENSOCUG00000000188	1 retrocopy	retro_ocun_1906,