RetrogeneDB ID: retro_cjac_3164

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:111770710..111771970(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022803
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TFDP2
• Ensembl ID: ENSCJAG00000001950
• Aliases: None
• Description: None

Sequence

>retro_cjac_3164
GGCAACATTTCATTTGTTGCATTTCCAGTTTCCAATACCAACTCACCTACAAAGATTTTACCAAAAACCTTAGGACCAAT
CAGTGTGAATGTTGGACCCCAAATGATTATAAGCACACCACAGAGACTAACCAGTTCAGGAAGTGTTCTGATTGGGAGTC
CATATACCCCTGCACCAGCAATGGTTACTCAGACACACATAGCAGAAGCTACTGGCTGGGTCCCTAGTGATAGAAAACGG
GCTAGAGAATTTATAGACTCTGATTTTTCAGAAAGTAAACGGAGCGAAAAAGGAGATAAAAATGGGAAAGGCTTGAGACA
CTTTTCAATGAAAGTGTGTGAGAAAGTTCAACGAAAAGGTACAACATCATACAATGAAGTCGCTGATGAGCTGGTGTCCG
AGTTCACCAATTCAAATAACCATGTGGCAGCTGATTCGCAGGCTTATGATCAGAAGAACATTAGGCGAAGAGTTTATGAT
GCTTTAAATGTACTAATGGCAATGAACATAATTTCAAAGGAAAAAAAAGAAATCAAGTGGATTGGCCTACCTACCAATTC
TGCTCAGGAATGTCAGAATCTGGAGATAGAAAAGCAGAGGCGGATAGAACGGATAAAGCAGAAGCGGGCCCAGCTGCAAG
AACTTCTCCTACAGCAAATTGCTTTCAAAAACCTGGTACAGAGAAATCGACAAAATGAACAGCAAAATCAGGGCCCTCCA
GCTCTGAACTCTACCATTCAGCTGCCATTTATAATTATCAATACAAGCAGAAAAACAGTCATAGATTGCAGCATCTCCAG
TGACAAGTTTGAGTATCTTTTCAATTTTGACAACACCTTTGAGATCCACGATGACATAGAAGTACTAAAGCGGATGGGAA
TGTCATTTGGTTTGGAGTCAGGCAAATGCTCTCTGGAGGATCTGAAACTTGCGAAATCTCTGGTGCCAAAGGCTTTAGAA
GGTTATATCACAGATATCTCCACAGGACCTTCTTGGTTAAATCAGGGACTACTTCTGAACTCTACCCAATCAGGTTCAAA
TTTAGACCTGACCACTGGTGCCACCTTACCCCAGTCAAGTGTAAACCAAGGGTTATGCTTGGATGCAGAAGTGGCCTTAG
CAACTGGGCAGTTCCTGGACCCAAACAGTCACCAGTCCAGCAGTGCAGCCTCTCACTACTCCGAGTCCCGAGGCGCGACC
CCCTGTTCATTCAATGATGAAGATGAGGAAGATGACGAGGAGGATTCCTCCTCCCCAGAA

Alignment

ORF - retro_cjac_3164 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.33 %
• Parental protein coverage: 93.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNISFVAFPVSNTNSPTKILPKTLGPINVNVGPQMIISTPQRLTSSGSVLIGSPYTPAPAMVTQTHIAEA
          GNISFVAFPVSNTNSPTKILPKTLGPI.VNVGPQMIISTPQRLTSSGSVLIGSPYTPAPAMVTQTHIAEA
Retrocopy GNISFVAFPVSNTNSPTKILPKTLGPISVNVGPQMIISTPQRLTSSGSVLIGSPYTPAPAMVTQTHIAEA

Parental  TGWVPSDRKRAREFIDSDFSESKRSKKGDKNGKGLRHFSMKVCEKVQRKGTTSYNEVADELVSEFTNSNN
          TGWVPSDRKRAREFIDSDFSESKRS.KGDKNGKGLRHFSMKVCEKVQRKGTTSYNEVADELVSEFTNSNN
Retrocopy TGWVPSDRKRAREFIDSDFSESKRSEKGDKNGKGLRHFSMKVCEKVQRKGTTSYNEVADELVSEFTNSNN

Parental  HLAADS-AYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEIEKQRRIERIKQKRA
          H.AADS.AYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEIEKQRRIERIKQKRA
Retrocopy HVAADSQAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEIEKQRRIERIKQKRA

Parental  QLQELLLQQIAFKNLVQRNRQNEQQNQGPPALNSTIQLPFIIINTSRKTVIDCSISSDKFEYLFNFDNTF
          QLQELLLQQIAFKNLVQRNRQNEQQNQGPPALNSTIQLPFIIINTSRKTVIDCSISSDKFEYLFNFDNTF
Retrocopy QLQELLLQQIAFKNLVQRNRQNEQQNQGPPALNSTIQLPFIIINTSRKTVIDCSISSDKFEYLFNFDNTF

Parental  EIHDDIEVLKRMGMSFGLESGKCSLEDLKLAKSLVPKALEGYITDISTGPSWLNQGLLLNSTQSGSNLDL
          EIHDDIEVLKRMGMSFGLESGKCSLEDLKLAKSLVPKALEGYITDISTGPSWLNQGLLLNSTQSGSNLDL
Retrocopy EIHDDIEVLKRMGMSFGLESGKCSLEDLKLAKSLVPKALEGYITDISTGPSWLNQGLLLNSTQSGSNLDL

Parental  TTGATLPQSSVNQGLCLDAEVALATGQFLAPNSHQSSSAASHCSESRGETPCSFNDEDEEDDEEDSSSPE
          TTGATLPQSSVNQGLCLDAEVALATGQFL.PNSHQSSSAASH.SESRG.TPCSFNDEDEEDDEEDSSSPE
Retrocopy TTGATLPQSSVNQGLCLDAEVALATGQFLDPNSHQSSSAASHYSESRGATPCSFNDEDEEDDEEDSSSPE

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	0.04 RPM	11.23 RPM
SRP051959_heart	0.02 RPM	16.49 RPM
SRP051959_kidney	0.13 RPM	15.82 RPM
SRP051959_liver	0.00 RPM	9.10 RPM
SRP051959_lung	0.07 RPM	14.46 RPM
SRP051959_lymph_node	0.05 RPM	11.44 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.67 RPM
SRP051959_spleen	0.23 RPM	17.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3164 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3164 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001950	1 retrocopy	retro_cjac_3164 ,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Otolemur garnettii	ENSOGAG00000000168	1 retrocopy	retro_ogar_2100,