RetrogeneDB ID: retro_cjac_364

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:76000437..76001391(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022272
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PRPS2
• Ensembl ID: ENSCJAG00000003885
• Aliases: None
• Description: Ribose-phosphate pyrophosphokinase [Source:UniProtKB/TrEMBL;Acc:F6S8U8]

Sequence

>retro_cjac_364
ATGCCGAATATCAAGATCTTCAGCGGCAGCTCCCACCAGGACTTATCTCAGAAAATTGCTGACCGCCTGGGCCTGGAGCT
AGGCAAGGTGGTGACTAAGAAATTCAGCAACCAGGAGACCTGTGTGGAAATTGGCGAGAGTGTACGTGGAGAGGATGTCT
ACATCGTTCAGAGTGGTTGTGGTGAAATCAATGACAATTTAATGGAGCTTTTGATCATGATTAATGCCTGCAAGATTGCT
TCAGCCAGCCGGGTTACTGCAGTCATCCCATGCTTCCCTTACGCCCGGCAGGATAAGAAAGATAAGAGCCGGGCGCCAAT
CTCAGCCAAGCTTGTTGCAAATATGCTATCTGTAGCAGGCGCAGATCATATTATCACCATGGACCTACACGCTTCTCAGA
TTCAGGGCTTTTTTGATATCCCAGTGGACAATTTGTATGCAGAGCCAGCTGTCCTAAAGTGGATAAGGGAGAATATCTCT
GAGTGGAGGAACTGCACTATTGTCTCACCTGATGCTGGTGGAGCGAAGAGAGTGACCTCCATTGCAGACAGGCTGAATGT
GGACTTTGCCTTGATTCACAAAGAACGGAAGAAGGCCAATGAAGTGGACCGCATGGTGCTTGTGGGAGATGTGAAGGATC
GGGTGGCCATCCTTGTGGATGACATGGCTGACACTTGTGGCACAATTTGCCATGCAGCTGACAAACTTCTCTCAGCTGGA
GCCACCAGAGTTTATGCCATCTTGACTCATGGAATCTTCTCCGGTCCGGCTATTTCTCGCATCAACAACGCATGCTTTGA
AGCAGTAGTAGTCACCAACACCATACCTCAGGAGGACAAGATGAAGCACTGCTCCAAAATACAAGTGATCGACATCTCTA
TGATTCTTGCAGAAGCCATCAGGAGAACTCACAATGGGGAATCCGTTTCTTACCTATTCAGCCATGTCCCTTTA

Alignment

ORF - retro_cjac_364 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNIVLFSGSSHQDLSQRVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEINDNLMEL
          MPNI..FSGSSHQDLSQ..ADRLGLELGKVVTKKFSNQET.VEIGESVRGEDVYI.QSGCGEINDNLMEL
Retrocopy MPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMEL

Parental  LIMINACKIASSSRVTAVIPCFPYARQDKKDKVGESRAPISAKLVANMLSVAGADHIITMDLHASQIQGF
          LIMINACKIAS.SRVTAVIPCFPYARQDKKDK...SRAPISAKLVANMLSVAGADHIITMDLHASQIQGF
Retrocopy LIMINACKIASASRVTAVIPCFPYARQDKKDK---SRAPISAKLVANMLSVAGADHIITMDLHASQIQGF

Parental  FDIPVDNLYAEPAVLQWIRENIAEWKNCIIVSPDAGGAKRVTSIADRLNVEFALIHKERKKANEVDRMVL
          FDIPVDNLYAEPAVL.WIRENI.EW.NC.IVSPDAGGAKRVTSIADRLNV.FALIHKERKKANEVDRMVL
Retrocopy FDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVL

Parental  VGDVKDRVAILVDDMADTCGTICHAADKLLSAGATKVYAILTHGIFSGPAISRINNAAFEAVVVTNTIPQ
          VGDVKDRVAILVDDMADTCGTICHAADKLLSAGAT.VYAILTHGIFSGPAISRINNA.FEAVVVTNTIPQ
Retrocopy VGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQ

Parental  EDKMKHCTKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
          EDKMKHC.KIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
Retrocopy EDKMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL

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	0.53 RPM	21.52 RPM
SRP051959_heart	0.72 RPM	5.82 RPM
SRP051959_kidney	0.87 RPM	43.09 RPM
SRP051959_liver	1.04 RPM	19.45 RPM
SRP051959_lung	1.07 RPM	18.97 RPM
SRP051959_lymph_node	1.37 RPM	35.11 RPM
SRP051959_skeletal_muscle	0.81 RPM	2.45 RPM
SRP051959_spleen	1.01 RPM	52.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_364 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_364 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011662	2 retrocopies	retro_cfam_1037, retro_cfam_1433,
Callithrix jacchus	ENSCJAG00000003885	1 retrocopy	retro_cjac_364 ,
Echinops telfairi	ENSETEG00000005166	2 retrocopies	retro_etel_1613, retro_etel_669,
Felis catus	ENSFCAG00000026323	1 retrocopy	retro_fcat_527,
Monodelphis domestica	ENSMODG00000017334	4 retrocopies	retro_mdom_1323, retro_mdom_1359, retro_mdom_258, retro_mdom_834,
Otolemur garnettii	ENSOGAG00000016087	1 retrocopy	retro_ogar_1440,
Procavia capensis	ENSPCAG00000001197	2 retrocopies	retro_pcap_219, retro_pcap_292,
Pongo abelii	ENSPPYG00000020125	1 retrocopy	retro_pabe_3431,
Pteropus vampyrus	ENSPVAG00000009452	1 retrocopy	retro_pvam_1224,
Sorex araneus	ENSSARG00000007710	1 retrocopy	retro_sara_18,
Ictidomys tridecemlineatus	ENSSTOG00000006056	1 retrocopy	retro_itri_1668,
Tupaia belangeri	ENSTBEG00000009917	1 retrocopy	retro_tbel_1245,
Tursiops truncatus	ENSTTRG00000003226	1 retrocopy	retro_ttru_1494,