RetrogeneDB ID: retro_cjac_3786

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01201331.1:445..1562(+)
• 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_3786
GTTTTTTTGCAGGATCCAGATGAAGAAATGGCCGAAATAGACAGGACGGTGAGGGACCAATGTGGGATCCAGGCTTGGGA
CAATAATGCAGTCTGTGCGGACCCCTGTTCCCTAATCCCCACACCTGACAAAGAAGATGATGAGCTGCTTTACCCAAACT
CAATGTGCAAGCCTCGGCATATCGCACCAGCCAGAGGTTCCCCACTGCCTGTACTGAGCTGGGCAAATAGAGAGGACGTC
TGGAAAATCATGTTAAACAAGGAAAAGACATACTTAAGGGATAAGCACTTTCTTGAGCAACATCCTCTTCTGCAGCCAAA
AATGCGAGCAATTCTGGATTGATTCATGGAGGTGTGTGAAGTCTGTAAGCCTCACAGGGAGACCTTTTACTTGGCACAAG
ATTTCTTTGACCGGTATATGGTGACACAAGAAAATGTCATAAAAACTCATTCACAGCTTATTGGGATTTCATCTTTATTT
ATAGCAGCCAAACTTGAGAAAATCTATCCTCCAAAGTTCCACCAGTTTGCTTATGTAACAGATGGAGCGTGTTCAGGAGA
TGAAATTCTTACCATGGAGTTAATGATTATGAAGGCCCTTAACTGGCATTTAAATCCCCTGACTATTGTATCCTGGCTGA
ATGTATACATGCAGATTGCATATCTAAATGACATCCATGAGGTGCTACTGCCGCAGTATCCCCAGCAAACCTTTATACAG
ATTGCAGAGCTGTTGGAGCTCTGTGTCCTGGATGTCGACTGCCTCGAATTTCCTTACAGTATACTCGCTGCTTCGGCCGT
GTATCATTTCTCTTCATCCGACTTGATGCAAAAGGTTTCAGGATATGAATGGTGCGACATAGAGAACTGTGCCAAGTGGA
TGGTTCCATTTGCCATGGTTATAAGGAAGACGGGGACCTCAAAACTGAAGCACTTCAGGGGCGTCGCTGATGAAGATGTG
CGCAATATACAGACCCACAGACAGCTTGGATTTACTGGACAAAGTCCGAGCAAAGAAAGCCATGTTGTCTGAACAAAATA
GGGCTTCTCCTCTCCCCAGTAGACTCCTCACCCCTCCACAGAGCAGTAAGAAGCAGAGCAATGGGCCAGAAATGGCA

Alignment

ORF - retro_cjac_3786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88. %
• Parental protein coverage: 91.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VFLQDPDEEMAKIDKTARDQCGSQAWDSNAVCADPCSLIPTPDKEEDELVYPNSMCKPRHIAPSRGSPLP
          VFLQDPDEEMA.ID.T.RDQCG.QAWD.NAVCADPCSLIPTPDKE.DEL.YPNSMCKPRHIAP.RGSPLP
Retrocopy VFLQDPDEEMAEIDRTVRDQCGIQAWDNNAVCADPCSLIPTPDKEDDELLYPNSMCKPRHIAPARGSPLP

Parental  VLSWANREEVWKIMLNKEKSYLRDKHFLEQHPLLQPKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRY
          VLSWANRE.VWKIMLNKEK.YLRDKHFLEQHPLLQPKMRAIL.D..MEVCEV.K.HRETFYLAQDFFDRY
Retrocopy VLSWANREDVWKIMLNKEKTYLRDKHFLEQHPLLQPKMRAIL-D*FMEVCEVCKPHRETFYLAQDFFDRY

Parental  MATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTMELMIMKALKWRLSPLTI
          M.TQENV.KT..QLIGISSLFIAAKLE.IYPPK.HQFAYVTDGACSGDEILTMELMIMKAL.W.L.PLTI
Retrocopy MVTQENVIKTHSQLIGISSLFIAAKLEKIYPPKFHQFAYVTDGACSGDEILTMELMIMKALNWHLNPLTI

Parental  VSWLNVYMQVAYLNDIHEVLLPQYPQQTFIQIAELLDLCVLDVDCLEFPYGILAASAVYHFSSSELMEKV
          VSWLNVYMQ.AYLNDIHEVLLPQYPQQTFIQIAELL.LCVLDVDCLEFPY.ILAASAVYHFSSS.LM.KV
Retrocopy VSWLNVYMQIAYLNDIHEVLLPQYPQQTFIQIAELLELCVLDVDCLEFPYSILAASAVYHFSSSDLMQKV

Parental  SGYEWCDIENCAKWMVPFAMVIRETGTSKLKHFRGVADEDAHNIQTHRDSLDLLDKARAKK-AMLSEQNR
          SGYEWCDIENCAKWMVPFAMVIR.TGTSKLKHFRGVADED..NIQTHR..L........K..AMLSEQNR
Retrocopy SGYEWCDIENCAKWMVPFAMVIRKTGTSKLKHFRGVADEDVRNIQTHR-QLGFTGQSPSKE>AMLSEQNR

Parental  ASPLPSGLLTPPQSSKKQSNGPEMA
          ASPLPS.LLTPPQSSKKQSNGPEMA
Retrocopy ASPLPSRLLTPPQSSKKQSNGPEMA

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_3786 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3786 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3786 has 0 orthologous retrocopies within eutheria group .

---

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,