RetrogeneDB ID: retro_cjac_457

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:116388222..116389232(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000012202
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000000157
• Aliases: None
• Description: None

Sequence

>retro_cjac_457
TCGGGCCCAGACGTCGAGACACCGTCCGCCATCCAGATCTGCCGGATCATGCGGCCAGATGACGCCAATGTGGCCGGCCA
TGTCCATGTGGGGACCATCCTGAAGATGATCGAGGAGGCGGGTGCCATCATCAGCACCCGGCATTGCAACAGCCAGAACG
GGGAGCGCTGTGTGGCTGCGCTGGCTCGGGTTGAGCGCACCGACTTCCTGTCGCCCATGTGCATCGGGGAGGTGGCCCAC
GTCAGTGCGGAAATCACCTATACCTCTAAGCACTCGGTGGAGGTACAGGTCAACGTGTTGTCTGAAAACATCCTCACAGG
TGCCAAAAAGCTGACCAATAAGGCCACCCTCTGGTATGTACCCCTGTCGCTGAAGAATGTGGACAAGGTCCTTGAGGTGC
CTCCTGTTGTGTATTCCCGGCAGGAGCAGGAGGAGGAGGGCCGAAAGCGATACGAAGCCCAGAAGCTGGAGCGCATGGAG
ACCAAGTGGAGGAACGGGGACATTGTCCAGCCAGTCCTCAACCCAGAGCCGAACACTGTCAGCTACAGCCAGTCCAGCTT
GATTCACCTGGTGGGGCCTTCAGACTGTACCCTACACGGCTTCGTCCATGGAGGTGTGACCATGAAGCTCATGGACGAGG
TCGCCGGGATCGTGGCTGCACGCCACTGCAAGACCAACATCGTCACAGCTTCCGTGGACGCCATTAATTTTCACGACAAG
ATCAGAAAAGGCTTCGTCATCACCATCTCAGGACGAATGACCTTCACGAGAATAAGTCCATGGAGATCGAGGTCTTGGTG
GACGCCGACCCTGTTGTGGACAGCTCGCAGAAGCGCTACCGGGCCGCCAGTGCCTTCTTCACCTACGTGTCGCTGAGCCA
GGAGGGCAGGTCGCTGCCCGTGCCCCAGCTTGTGCCTGAGACCGAGGACGAGAAGAAGCGCTTTGAGGAAGGCAAAGGGC
GGTACCTGCAGATGAAGGCGAAACGACAGGGCCACGCGGAGCCCCAGCCC

Alignment

ORF - retro_cjac_457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.8 %
• Parental protein coverage: 89.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGPRADLPPSGAYTTARIMRPDDANVAGNVHGGTILKMIEEAGAIISTRHCNSQNGERCVAALARVERTD
          .GP....P...A....RIMRPDDANVAG.VH.GTILKMIEEAGAIISTRHCNSQNGERCVAALARVERTD
Retrocopy SGPDVETP--SAIQICRIMRPDDANVAGHVHVGTILKMIEEAGAIISTRHCNSQNGERCVAALARVERTD

Parental  FLSPMCIGEVAHVSAEITYTSKHSVEVQVNVLSENILTGAKKLTNNATLWYVP-SLKNVDNKVLEVPPVV
          FLSPMCIGEVAHVSAEITYTSKHSVEVQVNVLSENILTGAKKLTN.ATLWYVP.SLKNVD.KVLEVPPVV
Retrocopy FLSPMCIGEVAHVSAEITYTSKHSVEVQVNVLSENILTGAKKLTNKATLWYVPLSLKNVD-KVLEVPPVV

Parental  FCRHSQQRSGPASKPASCLSRFGTPWHEGDAGQGILLPEPNTVSYSQSSLIHLVGPSDCTLHGFVHGGVT
          ..R..Q...G.....A..L.R..T.W..GD..Q..L.PEPNTVSYSQSSLIHLVGPSDCTLHGFVHGGVT
Retrocopy YSRQEQEEEGRKRYEAQKLERMETKWRNGDIVQPVLNPEPNTVSYSQSSLIHLVGPSDCTLHGFVHGGVT

Parental  MKLMDEVAGIVAARHCKTNIVTASVDAINFHDKIRKGFVITISGRMTFT-SNKSMEIEVLVDADPVVDSS
          MKLMDEVAGIVAARHCKTNIVTASVDAINFHDKIRKGFVITISGRMTFT..NKSMEIEVLVDADPVVDSS
Retrocopy MKLMDEVAGIVAARHCKTNIVTASVDAINFHDKIRKGFVITISGRMTFT<ENKSMEIEVLVDADPVVDSS

Parental  QKRYRAASAFFTYVSLSQEGRSLPVPQLVPETEDEKKRFEEGKGRYLQMKAKRQGHVEPQP
          QKRYRAASAFFTYVSLSQEGRSLPVPQLVPETEDEKKRFEEGKGRYLQMKAKRQGH.EPQP
Retrocopy QKRYRAASAFFTYVSLSQEGRSLPVPQLVPETEDEKKRFEEGKGRYLQMKAKRQGHAEPQP

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	9.54 RPM	28.93 RPM
SRP051959_heart	1.98 RPM	6.26 RPM
SRP051959_kidney	5.13 RPM	14.84 RPM
SRP051959_liver	4.51 RPM	12.48 RPM
SRP051959_lung	1.81 RPM	4.93 RPM
SRP051959_lymph_node	1.69 RPM	5.37 RPM
SRP051959_skeletal_muscle	1.53 RPM	4.65 RPM
SRP051959_spleen	2.63 RPM	6.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_457 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_457 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000157	2 retrocopies	retro_cjac_1229, retro_cjac_457 ,
Homo sapiens	ENSG00000097021	1 retrocopy	retro_hsap_3034,
Mustela putorius furo	ENSMPUG00000006882	1 retrocopy	retro_mputfur_177,
Nomascus leucogenys	ENSNLEG00000010371	1 retrocopy	retro_nleu_845,
Pongo abelii	ENSPPYG00000001945	1 retrocopy	retro_pabe_2513,
Pan troglodytes	ENSPTRG00000000084	1 retrocopy	retro_ptro_2047,