RetrogeneDB ID: retro_cjac_2209

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:10457416..10459340(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000035240
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WHSC1L1
• Ensembl ID: ENSCJAG00000002489
• Aliases: None
• Description: None

Sequence

>retro_cjac_2209
TTCTCTTTCATGCGAGGGATCATGGGAAACACAATTCAGCAACCACCTCAACTCATTGACTCCACCAACATCCGTCAGGA
GGATGCCTTTGATAACAACAGTGACATTGCTGAAGATGGTGGCCAGACACCCTATGAAGCTACCTTGCAGCAAGGTTTTC
AGTACCCAGCTACAACAGAAGATCTTCCTCCACTCACAAATGGCTATCCATCATCAGTCAGCATGTATGAACCTCAAACC
AAATACCAGTCGTATAATCAATATCCTAATGGGTCAGCCAGTGGCTTTGGTGCAGTTAGAAACTTTAGCCCCACTGACTA
TTACCATTCGGAAATTCCAAACACAAGACCACATGAAATTCTGGAAAAACCTTCCCCTCCACAGCCACCACCTCCTCCTT
CGGTACCACAAACGGTGATTCCAAAGAAGACTGGCTCACCTGAAATTAAACTAAAAATCACCAAAACTATCCAGAATGGC
AGGGAATTGTTTGAGCCTTCCCTTTGTGGAGACCTTTTAAATGAAGTACAGGCAAGTGAGCACACCAAGTCAAAGCATGA
AAGCAGAAAAGAAAAGAGAAAAAAAAAGCAACAAGCATGACTCATCGAGATCTGAAGAGCGCAAGTCACACAAAATCCCC
AAATTAGAACCAGAGGAACAAAATAGACCAAATGAGAGGGTTGACAGTGTAGCAGAAAAACCAAGGGAAGATCCAGTACT
AAAAGAGGAAGCCCCGGTTCAGCCAATACTATCTTCTCTTCCAACAACCGAAGTGTCCACTGGTGTTAAGTTTCAGGTTG
GTGATCTTGTGTGGTCCAAGGTGGGAACCTATCCTTGGTGGCCTTGTATGGTTTCAAGTGATCCCCAGCTTGAGGTTCAT
ACCAAAATTAACACAAGAGCTGCACGAGAATATCATGTCCAGTTTTTTAGCAACCAGCCAGAGAGAGCGTGGGTTCATGA
AAAACGGGTACGGGAGTATAAAGGTCATAAACAGTATGAAGAATTACTGGCTGAGGCAACCAAACAAGCCAGCAATCACT
CTGAGAAACAAAAGATTCGGAAACCTCGACCTCAGAGAGAACGTGCTCAGTGGGATATTGGCATTGCCCATGCAGAGAAA
GCATTGAAAATGACTAGAGAAGAAAGAATAGAACAGTATACTTTTATCTATATTGATAAACAGCCTGAAGAGGCTTTATC
CCAAGCAGAAAAGAATGTTGCCTCCAAAACTGAAGTTAAAAAAACCCGACAACCTGGATCTGTGCTGAATACTCAACCAG
AACAGACCAATGAAGGGGAGGTGGCCTCCTCACTCTCAAGTACTGAAATTCGGAGCCATAGCCAGAGGCGGCACACAAGT
GTGGAAGAGAAAGAGCCACCTCCTGTTAAAATAGCCTGGAAAACTGCGGCAGCAAGGAAATCCTTACCAGCTTCCATTAC
AATGCACAAAGGGAGCCTGGATTTGCAGAAGTGTAACATGACTCCAGTTGTGAAAATTGAACAAGTGTTTGCTCTTCAGA
ATGCTACAGGGGATGGGAAAGTTATCGATCCATTTGTTTACTCAACAAAGGGAATTGGTAACAAAACAGAAATAAGTGTC
AGGGGGCAAGACAGGCTCATAATTTCTACACCAAACCAGAGAAATGAAAAGCCAACGCAGAGTGTATCATCTCCTGAAGC
AACATCTGGTTCTACAGGCTCAGTAGAAAAGAAGCAACAGAGAAGATCAATTAGAACTCGTTCTGAATCAGAGAAATCCA
CTGAGGTCGTGCCAAAGAAGAAGATCAAAAAGGAGCAGGTTGAAATAGTTCATCAGGCTACAGTGAAGACTGGATTACAG
AAAGGGTCGGAGGACCGGGGAGTGCAGGGCTCTGTCAGATTCAGTGACAGCTCCGTCTCCGCAGCGATTGAGGAAACTGT
GGAC

Alignment

ORF - retro_cjac_2209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.73 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FSFMQGIMGNTIQQPPQLIDSANIRQEDAFDNNSDIAEDGGQTPYEATLQQGFQYPSTTEDLPPLTNGYP
          FSFM.GIMGNTIQQPPQLIDS.NIRQEDAFDNNSDIAEDGGQTPYEATLQQGFQYP.TTEDLPPLTNGYP
Retrocopy FSFMRGIMGNTIQQPPQLIDSTNIRQEDAFDNNSDIAEDGGQTPYEATLQQGFQYPATTEDLPPLTNGYP

Parental  SSISMYEPQTKYQSYNQYPNGSANGFGAVRNFSPTDYYHSEIPNTRPHEILEKPSPPQPPPPPSVPQTVI
          SS.SMYEPQTKYQSYNQYPNGSA.GFGAVRNFSPTDYYHSEIPNTRPHEILEKPSPPQPPPPPSVPQTVI
Retrocopy SSVSMYEPQTKYQSYNQYPNGSASGFGAVRNFSPTDYYHSEIPNTRPHEILEKPSPPQPPPPPSVPQTVI

Parental  PKKTGSPEIKLKITKTIQNGRELFESSLCGDLLNEVQASEHTKSKHESRKEKRKK-SNKHDSSRSEERKS
          PKKTGSPEIKLKITKTIQNGRELFE.SLCGDLLNEVQASEHTKSKHESRKEKRKK.SNKHDSSRSEERKS
Retrocopy PKKTGSPEIKLKITKTIQNGRELFEPSLCGDLLNEVQASEHTKSKHESRKEKRKK>SNKHDSSRSEERKS

Parental  HKIPKLEPEEQNRPNERVDSVAEKPREDPVLKEEAPVQPILSSVPTTEVSTGVKFQVGDLVWSKVGTYPW
          HKIPKLEPEEQNRPNERVDSVAEKPREDPVLKEEAPVQPILSS.PTTEVSTGVKFQVGDLVWSKVGTYPW
Retrocopy HKIPKLEPEEQNRPNERVDSVAEKPREDPVLKEEAPVQPILSSLPTTEVSTGVKFQVGDLVWSKVGTYPW

Parental  WPCMVSSDPQLEVHTKINTRGAREYHVQFFSNQPERAWVHEKRVREYKGHKQYEELLAEATKQASNHSEK
          WPCMVSSDPQLEVHTKINTR.AREYHVQFFSNQPERAWVHEKRVREYKGHKQYEELLAEATKQASNHSEK
Retrocopy WPCMVSSDPQLEVHTKINTRAAREYHVQFFSNQPERAWVHEKRVREYKGHKQYEELLAEATKQASNHSEK

Parental  QKIRKPRPQRERAQWDIGIAHAEKALKMTREERIEQYTFIYIDKQPEEALSQAKKNVASKTEVKKTRRPR
          QKIRKPRPQRERAQWDIGIAHAEKALKMTREERIEQYTFIYIDKQPEEALSQA.KNVASKTEVKKTR.P.
Retrocopy QKIRKPRPQRERAQWDIGIAHAEKALKMTREERIEQYTFIYIDKQPEEALSQAEKNVASKTEVKKTRQPG

Parental  SVLNTQPEQTNAGEVASSLSSTEIRRHSQRRHTSVEEEEPPPVKIAWKTAAARKSLPASITMHKGSLDLQ
          SVLNTQPEQTN.GEVASSLSSTEIR.HSQRRHTSVEE.EPPPVKIAWKTAAARKSLPASITMHKGSLDLQ
Retrocopy SVLNTQPEQTNEGEVASSLSSTEIRSHSQRRHTSVEEKEPPPVKIAWKTAAARKSLPASITMHKGSLDLQ

Parental  KCNMSPVVKIEQVFALQNATGDGKFIDQFVYSTKGIGNKTEISVRGQDRLIISTPNQRNEKPTQSVSSPE
          KCNM.PVVKIEQVFALQNATGDGK.ID.FVYSTKGIGNKTEISVRGQDRLIISTPNQRNEKPTQSVSSPE
Retrocopy KCNMTPVVKIEQVFALQNATGDGKVIDPFVYSTKGIGNKTEISVRGQDRLIISTPNQRNEKPTQSVSSPE

Parental  ATSGSTGSVEKKQQRRSIRTRSESEKSTEVVPKKKIKKEQVETVPQATVKTGLQKGSADRGVQGSVRFSD
          ATSGSTGSVEKKQQRRSIRTRSESEKSTEVVPKKKIKKEQVE.V.QATVKTGLQKGS.DRGVQGSVRFSD
Retrocopy ATSGSTGSVEKKQQRRSIRTRSESEKSTEVVPKKKIKKEQVEIVHQATVKTGLQKGSEDRGVQGSVRFSD

Parental  SSVSAAIEETVD
          SSVSAAIEETVD
Retrocopy SSVSAAIEETVD

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	0.35 RPM	51.39 RPM
SRP051959_heart	0.25 RPM	52.59 RPM
SRP051959_kidney	0.18 RPM	57.77 RPM
SRP051959_liver	0.26 RPM	33.08 RPM
SRP051959_lung	0.34 RPM	82.48 RPM
SRP051959_lymph_node	0.32 RPM	96.41 RPM
SRP051959_skeletal_muscle	0.09 RPM	23.59 RPM
SRP051959_spleen	0.34 RPM	72.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2209 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2209 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	ENSCJAG00000002489	1 retrocopy	retro_cjac_2209 ,
Callithrix jacchus	ENSCJAG00000037618	1 retrocopy	retro_cjac_3152,