RetrogeneDB ID: retro_cjac_3989

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286567.1:42520..43203(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000000050
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SCLY
• Ensembl ID: ENSCJAG00000000471
• Aliases: None
• Description: selenocysteine lyase [Source:HGNC Symbol;Acc:18161]

Sequence

>retro_cjac_3989
GGAAGAAAGGCCGAAGACATTATGAAAGCAGCTCGGGAGAGCCTTGCGAAGATGATTGGTGGGAAACCTCAAGACATCAT
CTTCACGTCCGGGGGCACTGAGTCAAATAATTGAGTAATCCATTCTGTGGTGAAACATTTCCACGTAAACCAGACCTCAA
AGGGAAACACGGGTGTGCACCACAGCCCAGTAGATGGGCCAAGCCCCATTTCATCACTTCCTCTGCGGAACACGACTCCA
TTCGACTACCCCTGGAGCACCTGGCAGAAGAACAAGCGGCAGCGGTCACCTTTGTCCCGGTGTCCAAGGCGAGCGGGCAG
GCAGAGGTAGACGACATCCTTGCAGCCGTCCGCCCGACCACACGCCTCGTGAGCATCATGCTGGCCAACAATGAGACCGG
CGTCGTCATTCCTGTCCCTGAAATCAGCCAACGCATTAAAGCCCTGAACCAGGAACGGGCAGCTGCCGGGCTGCCTCCCA
TCCTTGTGCACACGGATGCTGCACAGGCCTTGGGGAAGCGGCGCGTCGATGTGGAGGACCTGGGCGTGGACTTCCTTACA
ATCGTGGGGCACAAGGTTTATGGTCCCAGGATTGGCGCACTTTATGTACGAGGACTTGGTGAATGTACCCTTCTCTACCC
TATGCTGTTTGGAGGTGGACAAGAACAGAATTTCAGGCCAGGG

Alignment

ORF - retro_cjac_3989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.63 %
• Parental protein coverage: 71.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRKAKDIIKAARESLAKMIGGKPQDIIFTSGGTESNNLVIHSVVKHFYVNQTSKGDTGVHHSPVDG-AKP
          GRKA.DI.KAARESLAKMIGGKPQDIIFTSGGTESNN.VIHSVVKHF.VNQTSKG.TGVHHSPVDG.AKP
Retrocopy GRKAEDIMKAARESLAKMIGGKPQDIIFTSGGTESNN*VIHSVVKHFHVNQTSKGNTGVHHSPVDG<AKP

Parental  HFITSSVEHDSIRLPLEHLAEEQAAAVTFVPVSKASGQAEVDDILAAVRPTTRLVSIMLANNETGVVMPV
          HFITSS.EHDSIRLPLEHLAEEQAAAVTFVPVSKASGQAEVDDILAAVRPTTRLVSIMLANNETGVV.PV
Retrocopy HFITSSAEHDSIRLPLEHLAEEQAAAVTFVPVSKASGQAEVDDILAAVRPTTRLVSIMLANNETGVVIPV

Parental  PEISQRIKALNQERAAAGLPPILVHTDAAQALGKRRVDVEDLGVDFLTIVGHKFYGPRIGALYVRGLGEC
          PEISQRIKALNQERAAAGLPPILVHTDAAQALGKRRVDVEDLGVDFLTIVGHK.YGPRIGALYVRGLGEC
Retrocopy PEISQRIKALNQERAAAGLPPILVHTDAAQALGKRRVDVEDLGVDFLTIVGHKVYGPRIGALYVRGLGEC

Parental  TLLHPMLFGGGQEQNFRPG
          TLL.PMLFGGGQEQNFRPG
Retrocopy TLLYPMLFGGGQEQNFRPG

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	0.69 RPM	3.13 RPM
SRP051959_heart	0.56 RPM	3.72 RPM
SRP051959_kidney	1.11 RPM	12.56 RPM
SRP051959_liver	0.50 RPM	10.83 RPM
SRP051959_lung	1.27 RPM	3.92 RPM
SRP051959_lymph_node	2.08 RPM	6.10 RPM
SRP051959_skeletal_muscle	0.24 RPM	3.19 RPM
SRP051959_spleen	1.03 RPM	4.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3989 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3989 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3989 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013824	2 retrocopies	retro_chof_1528, retro_chof_1707,
Callithrix jacchus	ENSCJAG00000000471	1 retrocopy	retro_cjac_3989 ,
Oryctolagus cuniculus	ENSOCUG00000002777	1 retrocopy	retro_ocun_405,
Tarsius syrichta	ENSTSYG00000002756	1 retrocopy	retro_tsyr_1779,