RetrogeneDB ID: retro_cjac_3321

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:84715299..84715929(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002847
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GSTP1
• Ensembl ID: ENSCJAG00000000879
• Aliases: None
• Description: glutathione S-transferase pi 1 [Source:HGNC Symbol;Acc:4638]

Sequence

>retro_cjac_3321
ATGCCGCCCTACACCGTGGTCTACTTCCCAGTTCGAGGCCGCTGCGAGGCCATGCGCATGCTGCTGGCGGACCAGGGCCA
GAGCTGGAAGGAGGAGGTGGTGAGCATGGAGACCTGGCAGCAGGGCTCACTCAAAGCCTCCTGCCTGTATGGCCAGCTCC
CCAAGTTCCAGGATGGAGACCTCACCCTGTACCAGTCCAATGCCATCTTGCGTCACCTGGGCCGCACCCTGGGGCTCTAT
GGGAAGGACCAGCGGGAGGCAGCCATGGTGGACGTGGTGAATGACGGCGTGGAGGACCTCCGCTGCAAATACGCCTCCCT
CATTTACACCAACTACGAGGCAGGCAAGGCTGACTATGTGAAGGCATTGCCCAGGCATCTGAAGCCTTTTGAGACGCTGC
TGTCCCAGAACCAGGGAGGCAAGACCTTCATTGTGGGCGACCAGGTCTCCTTCGCCGACTACAACCTGCTGGACTTGCTG
CTGATCCATCAGGTTCTGGCCCCCAGCTGCCTGGATGCGTTCCCCCTGCTCTCGGCGTACGTGGAGCGCCTCTGCGCCCG
GCCCAAGCTCAAGGCCTTCCTGGCCTCCCCTGAGCACGTGAACCTCCCGATCAATGGCAATGGGAAACAG

Alignment

ORF - retro_cjac_3321 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MPPYTVVYFPVRGRCEAMRMLLADQGQSWKEEVVSMETWQQGSLKASCLYGQLPKFQDGDLTLYQSNAIL
          MPPYTVVYFPVRGRCEAMRMLLADQGQSWKEEVVSMETWQQGSLKASCLYGQLPKFQDGDLTLYQSNAIL
Retrocopy MPPYTVVYFPVRGRCEAMRMLLADQGQSWKEEVVSMETWQQGSLKASCLYGQLPKFQDGDLTLYQSNAIL

Parental  RHLGRTLGLYGKDQREAAMVDVVNDGVEDLRCKYASLIYTNYEAGKADYVKALPRHLKPFETLLSQNQGG
          RHLGRTLGLYGKDQREAAMVDVVNDGVEDLRCKYASLIYTNYEAGKADYVKALPRHLKPFETLLSQNQGG
Retrocopy RHLGRTLGLYGKDQREAAMVDVVNDGVEDLRCKYASLIYTNYEAGKADYVKALPRHLKPFETLLSQNQGG

Parental  KTFIVGDQVSFADYNLLDLLLIHQVLAPSCLDAFPLLSAYVERLCARPKLKAFLASPEHVNLPINGNGKQ
          KTFIVGDQVSFADYNLLDLLLIHQVLAPSCLDAFPLLSAYVERLCARPKLKAFLASPEHVNLPINGNGKQ
Retrocopy KTFIVGDQVSFADYNLLDLLLIHQVLAPSCLDAFPLLSAYVERLCARPKLKAFLASPEHVNLPINGNGKQ

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	0.64 RPM	43.62 RPM
SRP051959_heart	0.30 RPM	28.33 RPM
SRP051959_kidney	0.31 RPM	27.11 RPM
SRP051959_liver	0.22 RPM	13.58 RPM
SRP051959_lung	0.33 RPM	28.00 RPM
SRP051959_lymph_node	0.39 RPM	32.17 RPM
SRP051959_skeletal_muscle	0.20 RPM	27.06 RPM
SRP051959_spleen	0.34 RPM	45.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3321 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3321 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3321 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001020	3 retrocopies	retro_amel_1921, retro_amel_249, retro_amel_778,
Canis familiaris	ENSCAFG00000011349	4 retrocopies	retro_cfam_143, retro_cfam_2043, retro_cfam_46, retro_cfam_617,
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321 ,
Callithrix jacchus	ENSCJAG00000003123	7 retrocopies	retro_cjac_1299, retro_cjac_2226, retro_cjac_2463, retro_cjac_2498, retro_cjac_3004, retro_cjac_3084, retro_cjac_811,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Macropus eugenii	ENSMEUG00000001519	2 retrocopies	retro_meug_1519, retro_meug_1762,
Mustela putorius furo	ENSMPUG00000004029	2 retrocopies	retro_mputfur_1215, retro_mputfur_1463,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521,
Oryctolagus cuniculus	ENSOCUG00000002230	1 retrocopy	retro_ocun_391,
Rattus norvegicus	ENSRNOG00000018237	4 retrocopies	retro_rnor_2140, retro_rnor_2567, retro_rnor_2842, retro_rnor_769,
Tursiops truncatus	ENSTTRG00000003746	1 retrocopy	retro_ttru_1416,
Vicugna pacos	ENSVPAG00000008003	1 retrocopy	retro_vpac_73,