RetrogeneDB ID: retro_cjac_3996

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286801.1:3286..4365(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNE1
• Ensembl ID: ENSCJAG00000001857
• Aliases: None
• Description: None

Sequence

>retro_cjac_3996
AATAGGACGGCGAGGGACCAATGTGGGAGCCAGGCTTGGGACAATAATGCAGTCTGTGCGGGCCCCTGCTCCCTAATCCC
CACACCTGACAAAGAATATGATGAGCTGCTTTACCCAAACTTAATGTGCAAGCCTCGGCATATCGCACCAGCCAGAGGTT
CCCCACTGCCTGTACTGAGCTGGGCAAATAGAGAGGACGTCTGGAAAATCATGTTAAACAAGGAAAAGACATACTTAAGG
GATAAGCACTTTCTTGAGCAACATCCTCTTCTGCAGCCAAAAATGCGAGCAATTCTGGATTGATTCATGGAGGTGTGTGA
AGTCTGTAAGCCTCACAGGGAGACCTTTTACTTGGCACAAGATTTCTTTGACTGGTATATGACTACACAAGAAAATGTCA
TAAAAACTCTTTTACAGCTTATTGGGATTTCATCTTTATTTATAGCAGCCAAACTTGAGGAAATCTATCCTCCAAAGTTC
CACCAGTTTGCTTATGTAATAGATGGAGCGTGTTCAGGAGATAAAATTCTTACCATGGAGTTAATGATTATGAAGTCCCT
TAAGTGGCGTTTAAGTCCCCTGACTATTGTGTCCTGGCTGAATGTATACATGCAGATTGCATATCTAAATGACATCCATG
AGGTGCTACTGCCGCAGTATCCCCAGCAAACCTTTATACAGATTGCAAAGCTGTTGGAGCTCTGTGTCCTGGATGTCGAC
TGCCTCGAATTTCCTTACGGTATACTTGCTGCTTCGGCCGTGTATCATTTCTCTTCATCCGACTTGATGCAAAAGGTTTC
AGGATATGAATGGTGAGACATAGAGAACTGTGCCAAGTGGATGGTTCCATTTGCCATGGTTTAAGGGAGACGGGGACCTC
AAAACTGAAGCACTTCAGGGGCGTCGCTGATGAAGATGCGCACAATATACAGACCCACAGAGACAGCTTGGATTTGCTGG
ACAAAGCCCGAGCAAAGAAAGCCATGTTGTCTGAACAAAATAGGGCTTCTCCTCTCCCCAGTAGGCTCCTCACCCCTCCA
CAGAGCAGTAAGAAGCAGAGCAATGGGCCAGAAATGGCA

Alignment

ORF - retro_cjac_3996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.44 %
• Parental protein coverage: 88.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DKTARDQCGSQAWDSNAVCADPCSLIPTPDKEEDELVYPNSMCKPRHIAPSRGSPLPVLSWANREEVWKI
          ..TARDQCGSQAWD.NAVCA.PCSLIPTPDKE.DEL.YPN.MCKPRHIAP.RGSPLPVLSWANRE.VWKI
Retrocopy NRTARDQCGSQAWDNNAVCAGPCSLIPTPDKEYDELLYPNLMCKPRHIAPARGSPLPVLSWANREDVWKI

Parental  MLNKEKSYLRDKHFLEQHPLLQPKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQ
          MLNKEK.YLRDKHFLEQHPLLQPKMRAIL.D..MEVCEV.K.HRETFYLAQDFFD.YM.TQENV.KTLLQ
Retrocopy MLNKEKTYLRDKHFLEQHPLLQPKMRAIL-D*FMEVCEVCKPHRETFYLAQDFFDWYMTTQENVIKTLLQ

Parental  LIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVAYL
          LIGISSLFIAAKLEEIYPPK.HQFAYV.DGACSGD.ILTMELMIMK.LKWRLSPLTIVSWLNVYMQ.AYL
Retrocopy LIGISSLFIAAKLEEIYPPKFHQFAYVIDGACSGDKILTMELMIMKSLKWRLSPLTIVSWLNVYMQIAYL

Parental  NDIHEVLLPQYPQQTFIQIAELLDLCVLDVDCLEFPYGILAASAVYHFSSSELMEKVSGYEWCDIENCAK
          NDIHEVLLPQYPQQTFIQIA.LL.LCVLDVDCLEFPYGILAASAVYHFSSS.LM.KVSGYEW.DIENCAK
Retrocopy NDIHEVLLPQYPQQTFIQIAKLLELCVLDVDCLEFPYGILAASAVYHFSSSDLMQKVSGYEW*DIENCAK

Parental  WMVPFAMV-IRETGTSKLKHFRGVADEDAHNIQTHRDSLDLLDKARAKKAMLSEQNRASPLPSGLLTPPQ
          WMVPFAMV..RETGTSKLKHFRGVADEDAHNIQTHRDSLDLLDKARAKKAMLSEQNRASPLPS.LLTPPQ
Retrocopy WMVPFAMV<LRETGTSKLKHFRGVADEDAHNIQTHRDSLDLLDKARAKKAMLSEQNRASPLPSRLLTPPQ

Parental  SSKKQSNGPEMA
          SSKKQSNGPEMA
Retrocopy SSKKQSNGPEMA

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	1.55 RPM
SRP051959_heart	0.00 RPM	0.65 RPM
SRP051959_kidney	0.00 RPM	0.29 RPM
SRP051959_liver	0.00 RPM	0.19 RPM
SRP051959_lung	0.00 RPM	0.75 RPM
SRP051959_lymph_node	0.00 RPM	1.23 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.55 RPM
SRP051959_spleen	0.00 RPM	0.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3996 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3996 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001593	1 retrocopy	retro_cjac_3884,
Callithrix jacchus	ENSCJAG00000001857	2 retrocopies	retro_cjac_3786, retro_cjac_3996 ,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Oryctolagus cuniculus	ENSOCUG00000009143	1 retrocopy	retro_ocun_676,
Otolemur garnettii	ENSOGAG00000006217	2 retrocopies	retro_ogar_3309, retro_ogar_930,
Sus scrofa	ENSSSCG00000002855	1 retrocopy	retro_sscr_232,
Vicugna pacos	ENSVPAG00000001390	1 retrocopy	retro_vpac_219,