RetrogeneDB ID: retro_cjac_2844

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:117060626..117061388(-)
• Located in intron of: ENSCJAG00000004698

Retrocopy information

• Ensembl ID: ENSCJAG00000035086
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000035427
• Aliases: None
• Description: None

Sequence

>retro_cjac_2844
GAAAGTATGGGCAGATCACACGTTGCTTCCCCCGGCCCTTGTCCTGACAGAATGCCCCCGCCATCACCCACTGAGTCTAG
GCACAGCCTCTCAATCCCTCCCTTCTCCAGCCCCCCAGAGCAGAAAGTGGGTCTTTACCAGAGACAAACTGAACTTCAAG
ACAAAAGTGAATTTTCAGATGTGGACGAGCTAGTTTTTAGGGATAATGAGAAATCTAAATCATCTTTTGAATATACAAGG
AACATGCCAAGGCGGTTTGAAATGGATGGGCTCTCTCCTGCCGGGGATATGCCTCATGTGGGCACTGCTGCAGCTGCTGT
GCCCCTCTCATATCAGCACCCAAGTGTACATCAGAAACAAATTGAAGAACAAAAGGAAGAAGAAAAAATATGGGAACAGC
AAGTGAAAGAACGAGGGCAGAGAGAAGAAAGAAGGCAGAGTAACCTACAAGAAATTTTAGAGAGGGAACGAAGAGAACTA
GAAAAACTGTATCAGGAAAGGAGGATGACTGAAGAATCACTGAAGATTGAAATGGAAAATGAATTAGAAGTGAGTAATCA
AGAAATGAAAGACAAATTTGTTCGCAGTGAAAACCCTTTAGAGAAATACATGAAAATCCTCCAGCAGGAGCAAGACCAGG
AGTCGGCAGATAAGAAGTCAAAAAACATGGTCCAAGAAGGCTCCCTAGTGGACACACTGCAGTCTAGTGACAAAGTAGAA
AGTTTAACAGACTCTCCTCATGAAGAACCAGATGACTCTTGG

Alignment

ORF - retro_cjac_2844 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.1 %
• Parental protein coverage: 93.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESLGRSHVASPSPCPDRMTLPSPTESRHSLSIAPFS-PPEQKAGLYQRQTELQNKSEFSDVDKLAFKDNE
          ES.GRSHVASP.PCPDRM..PSPTESRHSLSI.PFS.PPEQK.GLYQRQTELQ.KSEFSDVD.L.F.DNE
Retrocopy ESMGRSHVASPGPCPDRMPPPSPTESRHSLSIPPFSSPPEQKVGLYQRQTELQDKSEFSDVDELVFRDNE

Parental  DSESSFEW--NVPRQFEMDGLSPAGDMPPVGTDAAAEPLSYQHPSIDQKQIDE-KEEEKIREQQVKERRQ
          .S.SSFE...N.PR.FEMDGLSPAGDMP.VGT.AAA.PLSYQHPS..QKQI.E.KEEEKI.EQQVKER.Q
Retrocopy KSKSSFEYTRNMPRRFEMDGLSPAGDMPHVGTAAAAVPLSYQHPSVHQKQIEEQKEEEKIWEQQVKERGQ

Parental  REERSQSNLQEILERERRELEKLDQERRMPDKSVKIEMENELEMSNQEMKDKSAHSENPLEKYMKIIQQE
          REER.QSNLQEILERERRELEKL.QERRM...S.KIEMENELE.SNQEMKDK...SENPLEKYMKI.QQE
Retrocopy REERRQSNLQEILERERRELEKLYQERRMTEESLKIEMENELEVSNQEMKDKFVRSENPLEKYMKILQQE

Parental  KDQELADKSSQKMVQEGSPVDTLQSSDKVESLTGFSPEEPDDSW
          .DQE.ADK.S..MVQEGS.VDTLQSSDKVESLT....EEPDDSW
Retrocopy QDQESADKKSKNMVQEGSLVDTLQSSDKVESLTDSPHEEPDDSW

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	5.15 RPM
SRP051959_heart	0.02 RPM	6.75 RPM
SRP051959_kidney	0.00 RPM	10.12 RPM
SRP051959_liver	0.00 RPM	5.70 RPM
SRP051959_lung	0.00 RPM	10.05 RPM
SRP051959_lymph_node	0.00 RPM	11.32 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.98 RPM
SRP051959_spleen	0.00 RPM	8.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2844 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2844 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2844 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035427	1 retrocopy	retro_cjac_2844 ,
Homo sapiens	ENSG00000046651	1 retrocopy	retro_hsap_3164,
Gorilla gorilla	ENSGGOG00000006453	1 retrocopy	retro_ggor_1352,
Nomascus leucogenys	ENSNLEG00000009180	1 retrocopy	retro_nleu_2496,
Pan troglodytes	ENSPTRG00000021675	1 retrocopy	retro_ptro_2274,