RetrogeneDB ID: retro_cjac_467

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:136737788..136738034(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYF2
• Ensembl ID: ENSCJAG00000018559
• Aliases: None
• Description: SYF2 homolog, RNA splicing factor (S. cerevisiae) [Source:HGNC Symbol;Acc:19824]

Sequence

>retro_cjac_467
AAATTACCTGCAAACTGGGAAGCTAATAAGCATCATTTCAAATGGGAATTGCAGGAAGAAGGAGGAAAAAAAAATGTTCA
GACAAAGACTATGAGAAAAGATACAGAAAGATGGGAGAGAAAAAAAAAAAGGAAAAACTTCAATCTGGGATTTTTACATT
ATGCTGCTTCCCAGTTGCACCAGTATCACTGGTTGACCAAGCAGATCAAACCTGACACAGAAATATATTAAAGACTAACA
GAAAAA

Alignment

ORF - retro_cjac_467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.38 %
• Parental protein coverage: 53.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KARLEWELQEEEKKKECAARGEDYEKVKLLEISAEDAERWERKKKRKNPDLGFSDYAAAQLRQYHRLTKQ
          K....WE......K.E.....E...K.........D.ERWERKKKRKN..LGF..YAA.QL.QYH.LTKQ
Retrocopy KLPANWEANKHHFKWEL--QEEGGKKNVQTKTMRKDTERWERKKKRKNFNLGFLHYAASQLHQYHWLTKQ

Parental  IKPDMETYERLREK
          IKPD.E.Y.RL.EK
Retrocopy IKPDTEIY*RLTEK

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	4.53 RPM
SRP051959_heart	0.00 RPM	6.47 RPM
SRP051959_kidney	0.00 RPM	7.94 RPM
SRP051959_liver	0.00 RPM	4.14 RPM
SRP051959_lung	0.02 RPM	7.84 RPM
SRP051959_lymph_node	0.00 RPM	6.94 RPM
SRP051959_skeletal_muscle	0.04 RPM	7.40 RPM
SRP051959_spleen	0.00 RPM	7.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_467 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_467 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_467 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4152

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010115	1 retrocopy	retro_amel_566,
Bos taurus	ENSBTAG00000001651	1 retrocopy	retro_btau_478,
Choloepus hoffmanni	ENSCHOG00000005273	1 retrocopy	retro_chof_2034,
Callithrix jacchus	ENSCJAG00000018559	1 retrocopy	retro_cjac_467 ,
Homo sapiens	ENSG00000117614	1 retrocopy	retro_hsap_4152,
Monodelphis domestica	ENSMODG00000013951	1 retrocopy	retro_mdom_899,
Oryctolagus cuniculus	ENSOCUG00000013050	1 retrocopy	retro_ocun_1522,
Sarcophilus harrisii	ENSSHAG00000007152	1 retrocopy	retro_shar_15,