RetrogeneDB ID: retro_cjac_1598

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:46510031..46510649(-)
• Located in intron of: ENSCJAG00000003426

Retrocopy information

• Ensembl ID: ENSCJAG00000003495
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTCD2
• Ensembl ID: ENSCJAG00000016364
• Aliases: None
• Description: None

Sequence

>retro_cjac_1598
GGTGCTTTGGAAGTCTTGATAGAGATGAAAAACCAAGATGTGAAGTTCACTGTAGATACCTATGTTCTTGCTTTTGCAAT
TTGCTATAAACTGAATAGCCCTGAGTCTTTTAAAATCTGTACTACATTAAGAGAAGAAGCCCTACTCAAAGGAGAAATTC
TCTCCAGGAGAGCATCCTGTTTCGCTGTGGCATTAGCTCTGAATCAGAATGAGGTAGCACAAGCTATGTCCATTTTTTCT
CAAATCATGAATTCAGAAAGCATAACCTGCACTAATTTAAATATTATACTCCATATCCAGTTAAATATGTTGGAAAACGT
GATAGAGATACTAAAAAATGCTACAGAAGGAAATTTATCAAAATATGTGAAGAGACAGGTGTTCTCAGAGGAAGTGCTGG
CCAAAGTGAGGGAAAAAGTGAAGGATGTGCCTGCCCTTGTGGCCAAATTTGATGAGCTCTATGGGAAACTGCACGTCAGT
GGCCAAGTCACCACTTATTCTTTGGATGCTGTGCTCTGCCACATCCCTGGGGGCAGGAAATCCCACATGTTTCTATTAAA
CAAGAGAATGGTCAGCCGTCGCACCTTCCAGCCACTCGGCCAGTCCCTGTTTGCTAAG

Alignment

ORF - retro_cjac_1598 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.06 %
• Parental protein coverage: 73.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GALEVLIEMKNQDVKFTVDTYVLAFAICYKLNSPESFKICSTLREEALLKGEILPRRASCFAVALALNQN
          GALEVLIEMKNQDVKFTVDTYVLAFAICYKLNSPESFKIC.TLREEALLKGEIL.RRASCFAVALALNQN
Retrocopy GALEVLIEMKNQDVKFTVDTYVLAFAICYKLNSPESFKICTTLREEALLKGEILSRRASCFAVALALNQN

Parental  EVAQAMSIFSQIMNPESITCTNLNIILHIQLNMLENVIEILKNATEGNLSKYVKRQVFSEEVLAKVREKV
          EVAQAMSIFSQIMN.ESITCTNLNIILHIQLNMLENVIEILKNATEGNLSKYVKRQVFSEEVLAKVREKV
Retrocopy EVAQAMSIFSQIMNSESITCTNLNIILHIQLNMLENVIEILKNATEGNLSKYVKRQVFSEEVLAKVREKV

Parental  KDVPALVAKFDELYGKLHVSGQVTTYSLDAVLCHIPGGRKSHMFLLNKRMVSRRTFQPLGQSLFAE
          KDVPALVAKFDELYGKLHVSGQVTTYSLDAVLCHIPGGRKSHMFLLNKRMVSRRTFQPLGQSLFA.
Retrocopy KDVPALVAKFDELYGKLHVSGQVTTYSLDAVLCHIPGGRKSHMFLLNKRMVSRRTFQPLGQSLFAK

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	0.16 RPM	6.48 RPM
SRP051959_heart	0.16 RPM	9.51 RPM
SRP051959_kidney	0.13 RPM	10.76 RPM
SRP051959_liver	0.19 RPM	6.13 RPM
SRP051959_lung	0.08 RPM	4.93 RPM
SRP051959_lymph_node	0.07 RPM	5.46 RPM
SRP051959_skeletal_muscle	0.07 RPM	7.73 RPM
SRP051959_spleen	0.06 RPM	7.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1598 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1598 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1598 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016364	1 retrocopy	retro_cjac_1598 ,
Homo sapiens	ENSG00000049883	2 retrocopies	retro_hsap_1388, retro_hsap_607,
Gorilla gorilla	ENSGGOG00000010695	2 retrocopies	retro_ggor_1077, retro_ggor_534,
Macaca mulatta	ENSMMUG00000017908	1 retrocopy	retro_mmul_2240,
Nomascus leucogenys	ENSNLEG00000004516	2 retrocopies	retro_nleu_2954, retro_nleu_436,
Otolemur garnettii	ENSOGAG00000008390	1 retrocopy	retro_ogar_3169,
Pan troglodytes	ENSPTRG00000016968	2 retrocopies	retro_ptro_447, retro_ptro_952,
Ictidomys tridecemlineatus	ENSSTOG00000006596	1 retrocopy	retro_itri_1469,