RetrogeneDB ID: retro_cjac_2339

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:54259463..54260992(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011208
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FH
• Ensembl ID: ENSCJAG00000017359
• Aliases: None
• Description: None

Sequence

>retro_cjac_2339
ATGTACCGAGCACTCCGGCTCCTCGCGCGCTCGCGTCGCCTCTCACGGGCTCCTGCCTCAGCCCCAGCGTCGGCTTCCGG
CTTGGGTGGCGTGGCCGTGCCCTCGTTTTGGCCCCCGAACGCGGCTCGAATGGCAAGCCAGAATTCCTTCCGGGTAGAAT
ATGATACGTTTGGTGAGCTAAAAGTGCCAAATGATAAGTACTATGGTGCCCAGACCGTGAGATCTACGATGAACTTTAAG
ATCGGAGGTGTGACAGAACGCATGCCAACCCCAGTTATTAAAGCTTTTGGCATCTTGAAGCGAGCGGCTGCTGAAGTAAA
CCAGGATTATGGTCTTGATCCAAAGATTGCCAATGCAATAATGAAGGCAGCAGATGAGGTAGCTGAAGGTAAATTAAATG
ATCATTTTCCTCTCGTGGTATGGCAGACTGGATCAGGAACTCAGACAAATATGAATGTAAATGAAGTCATTAGCAATAGA
GCAATTGAAATGTTAGGAGGTGAACTTGGCAGCAAGAAACCTGTGCATCCCAATGATCATGTTAATAAAAGCCAGAGCTC
AAATGATACTTTTCCCACAGCAATGCACATTGCTGCTGCAACAGAAGTTCATGAAGTACTGTTACCAGGACTACAGAAAC
TGCACATGCTCTTGATGCCAAATCCAAAGAGTTTGCACAGATCATTAAAATTGGGCGCACTCACACTCAGGACGCTGTTC
CACTGACTCTTGGGCAGGAATTTAGTGGTTATGTTCAACAAGTGAAATATGCAATGTCAAGAATAAAAGCTGCCATGCCA
AGAATCTATGAGCTCGCAGCTGGAGGCACTGCTGTTGGTACAGGTTTAAATACTAGAATTGGCTTTGCAGAAAAGGTTGC
TGCAAAAGTGGCTGCACTTACGGGCTTGCCTTTTGTCACTGCTCCAAATAAATTTGAAGCTCTGGCTGCTCATGACGCTC
TGGTTGAGCTCAGTGGAGCCATGAACACTACTGCCTGCAGTCTGATGAAGATAGCAAATGATATTCGTTTTCTGGGTTCT
GGTCCTCGGTCAGGTCTGGGAGAACTGATCTTGCCTGAAAATGAACCAGGAAGCAGTATCATGCCAGGCAAGGTGAACCC
TACTCAGTGTGAAGCAATGACCATGGTTGCAGCCCAAGTCATGGGGAATCACGTTGCTGTAACTGTCGGAGGCAGCAATG
GACATTTTGAGTTGAATGTTTTCAAGCCAATGATGATTAAAAATGTGTTACACTCAGCCCGGCTGCTGGGGGATGCTTCA
GTTTCCTTTACAGAAAACTGTGTGGTGGGAATCCAGGCCAATACAGAAAGGATCAACAAGCTGATGAATGAGTCTCTAAT
GTTGGTGACAGCTCTCAATCCTCACATAGGTTATGACAAGGCAGCAAAGATTGCTAAGACAGCACACAAAAATGGATCCA
CCTTAAAGGAAACCGCTATTGAACTTGGCTATCTCACAGCAGAGCAGTTTGACGAATGGGTAAAACCTAAGGACATGCTG
GGTCCAAAG

Alignment

ORF - retro_cjac_2339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYRALRLLARSRRLSRAPASAPASASGLGGAAVPSFWPPNAARMASQNSFRVEYDTFGELKVPNDKYYGA
          MYRALRLLARSRRLSRAPASAPASASGLGG.AVPSFWPPNAARMASQNSFRVEYDTFGELKVPNDKYYGA
Retrocopy MYRALRLLARSRRLSRAPASAPASASGLGGVAVPSFWPPNAARMASQNSFRVEYDTFGELKVPNDKYYGA

Parental  QTVRSTMNFKIGGVTERMPTPVIKAFGILKRAAAEVNQDYGLDPKIANAIMKAADEVAEGKLNDHFPLVV
          QTVRSTMNFKIGGVTERMPTPVIKAFGILKRAAAEVNQDYGLDPKIANAIMKAADEVAEGKLNDHFPLVV
Retrocopy QTVRSTMNFKIGGVTERMPTPVIKAFGILKRAAAEVNQDYGLDPKIANAIMKAADEVAEGKLNDHFPLVV

Parental  WQTGSGTQTNMNVNEVISNRAIEMLGGELGSKKPVHPNDHVNKSQSSNDTFPTAMHIAAATEVHEVLLPG
          WQTGSGTQTNMNVNEVISNRAIEMLGGELGSKKPVHPNDHVNKSQSSNDTFPTAMHIAAATEVHEVLLPG
Retrocopy WQTGSGTQTNMNVNEVISNRAIEMLGGELGSKKPVHPNDHVNKSQSSNDTFPTAMHIAAATEVHEVLLPG

Parental  LQKLH-DALDAKSKEFAQIIKIGRTHTQDAVPLTLGQEFSGYVQQVKYAMSRIKAAMPRIYELAAGGTAV
          LQKLH..ALDAKSKEFAQIIKIGRTHTQDAVPLTLGQEFSGYVQQVKYAMSRIKAAMPRIYELAAGGTAV
Retrocopy LQKLH<HALDAKSKEFAQIIKIGRTHTQDAVPLTLGQEFSGYVQQVKYAMSRIKAAMPRIYELAAGGTAV

Parental  GTGLNTRIGFAEKVAAKVAALTGLPFVTAPNKFEALAAHDALVELSGAMNTTACSLMKIANDIRFLGSGP
          GTGLNTRIGFAEKVAAKVAALTGLPFVTAPNKFEALAAHDALVELSGAMNTTACSLMKIANDIRFLGSGP
Retrocopy GTGLNTRIGFAEKVAAKVAALTGLPFVTAPNKFEALAAHDALVELSGAMNTTACSLMKIANDIRFLGSGP

Parental  RSGLGELILPENEPGSSIMPGKVNPTQCEAMTMVAAQVMGNHVAVTVGGSNGHFELNVFKPMMIKNVLHS
          RSGLGELILPENEPGSSIMPGKVNPTQCEAMTMVAAQVMGNHVAVTVGGSNGHFELNVFKPMMIKNVLHS
Retrocopy RSGLGELILPENEPGSSIMPGKVNPTQCEAMTMVAAQVMGNHVAVTVGGSNGHFELNVFKPMMIKNVLHS

Parental  ARLLGDASVSFTENCVVGIQANTERINKLMNESLMLVTALNPHIGYDKAAKIAKTAHKNGSTLKETAIEL
          ARLLGDASVSFTENCVVGIQANTERINKLMNESLMLVTALNPHIGYDKAAKIAKTAHKNGSTLKETAIEL
Retrocopy ARLLGDASVSFTENCVVGIQANTERINKLMNESLMLVTALNPHIGYDKAAKIAKTAHKNGSTLKETAIEL

Parental  GYLTAEQFDEWVKPKDMLGPK
          GYLTAEQFDEWVKPKDMLGPK
Retrocopy GYLTAEQFDEWVKPKDMLGPK

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	0.38 RPM	9.63 RPM
SRP051959_heart	0.40 RPM	17.59 RPM
SRP051959_kidney	0.80 RPM	17.19 RPM
SRP051959_liver	0.58 RPM	25.62 RPM
SRP051959_lung	0.59 RPM	6.52 RPM
SRP051959_lymph_node	0.89 RPM	7.28 RPM
SRP051959_skeletal_muscle	0.33 RPM	22.80 RPM
SRP051959_spleen	0.63 RPM	7.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2339 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2339 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2339 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017359	1 retrocopy	retro_cjac_2339 ,
Echinops telfairi	ENSETEG00000018721	2 retrocopies	retro_etel_1069, retro_etel_1457,
Microcebus murinus	ENSMICG00000003451	2 retrocopies	retro_mmur_1215, retro_mmur_720,
Mus musculus	ENSMUSG00000026526	1 retrocopy	retro_mmus_3600,
Oryctolagus cuniculus	ENSOCUG00000021494	1 retrocopy	retro_ocun_50,
Otolemur garnettii	ENSOGAG00000009936	1 retrocopy	retro_ogar_322,
Rattus norvegicus	ENSRNOG00000003653	1 retrocopy	retro_rnor_2979,
Xenopus tropicalis	ENSXETG00000032112	1 retrocopy	retro_xtro_55,