RetrogeneDB ID: retro_cjac_1389

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:29146826..29147885(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007390
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BRIX1
• Ensembl ID: ENSCJAG00000018506
• Aliases: None
• Description: None

Sequence

>retro_cjac_1389
ATGGCGGCAACCAAGAGGAAACGGCGTGGAGGCTTGGCAGTTCAGGCAAAGAAGCCAAAAAGAAACGAGAAAGATGCCGA
ACCGCCAGCTAAGCCTCGAGCCACTGCAGAGGAGGTGGAGGAAGAAGAGAGAAACCGGATCCCAGGCCCCGTTTGCAAGG
GCAAGTGGAAAAATAAGGAACGGATTCTCATCTTTTCTTCCAGAGGAATACATTTCAGAACAAGACATTTAATGCAGGAC
TTGAGAAGGTTGATGCCTCATTCTAAAGCGGATACTAAAATGGATCGTAAGGATAAGCTATTTGTGATTAACGAGGTTTG
TGAAATGAAAAACTGTAATAAATGCATCTATTTTGAAGCTAAGAAAAAACAGGATCTCTATATGTGGCTTTCAAACTCAC
CTCATGGACCATCTGCTAAATTCCTTGTTCAAAATATTCATACCCTTGCTGAACTAAAGATGACTGGAAACTGTTTGAAA
GGTTCTCGGCCCCTTTTGTCTTTTGACCCAGCTTTTGATGAATTACCACATTATGCTTTGTTAAAAGAACTCTTAATTCA
GATCTTTAGTACACCACGGTATCATCCCAAAAGCCAACCATTCGTGGACCATGTGTTTCCTTTCACGATTTTGGATAATA
GGATATGGTTTCGGAACTTTCAGATTACAGAAGAAGATGCTGCTCTTGTAGAAATAGGACCTCGTTTTGTCTTAAGTCTC
ATAAAGATTTTCCAGGGAAGTTTTGGAGGACCAACTTTATATGAAAACCCTCACTACCAGTCACCAAACATGCATCGGCA
TGTCATAAGATCCATCACAGCTGCAAAATACAAAGAGAAACAGCAAGTGAAAGATGTGCAGAAACTGAGAAAGAAAGAAC
TGAAGACTCTTCTTCCACACGATCCCACTGCAGGTGTTTTTGTTATGCCAGCCGAGGAGAAACCAATAGAAATACAGTGG
GTAAAGCCAGAGCCAAAAGTTGATTTGAAAGCACGAAAAAAACGGATTTACAAAAGGCAAAGAAAAATGAAACAGAGGAT
GGACAGAAGGAAAACAAAA

Alignment

ORF - retro_cjac_1389 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAATKRKRRGGLAVQAKKPKRNEKDAEPPAKPRATAEEVEEEERNRIPGPVCKGKWKNKERILIFSSRGI
          MAATKRKRRGGLAVQAKKPKRNEKDAEPPAKPRATAEEVEEEERNRIPGPVCKGKWKNKERILIFSSRGI
Retrocopy MAATKRKRRGGLAVQAKKPKRNEKDAEPPAKPRATAEEVEEEERNRIPGPVCKGKWKNKERILIFSSRGI

Parental  NFRTRHLMQDLRRLMPHSKADTKMDRKDKLFVINEVCEMKNCNKCIYFEAKKKQDLYMWLSNSPHGPSAK
          .FRTRHLMQDLRRLMPHSKADTKMDRKDKLFVINEVCEMKNCNKCIYFEAKKKQDLYMWLSNSPHGPSAK
Retrocopy HFRTRHLMQDLRRLMPHSKADTKMDRKDKLFVINEVCEMKNCNKCIYFEAKKKQDLYMWLSNSPHGPSAK

Parental  FLVQNIHTLAELKMTGNCLKGSRPLLSFDPAFDELPHYALLKELLIQIFSTPRYHPKSQPFVDHVFTFTI
          FLVQNIHTLAELKMTGNCLKGSRPLLSFDPAFDELPHYALLKELLIQIFSTPRYHPKSQPFVDHVF.FTI
Retrocopy FLVQNIHTLAELKMTGNCLKGSRPLLSFDPAFDELPHYALLKELLIQIFSTPRYHPKSQPFVDHVFPFTI

Parental  LDNRIWFRNFQIIEEDAALVEIGPRFVLNLIKIFQGSFGGPTLYENPHYQSPNMHRRVIRSITAAKYKEK
          LDNRIWFRNFQI.EEDAALVEIGPRFVL.LIKIFQGSFGGPTLYENPHYQSPNMHR.VIRSITAAKYKEK
Retrocopy LDNRIWFRNFQITEEDAALVEIGPRFVLSLIKIFQGSFGGPTLYENPHYQSPNMHRHVIRSITAAKYKEK

Parental  QQVKDVQKLRKKELKTLLPHDPTADVFVTPADEKPIEIQWVKPEPKVDLKARKKRIYKRQRKMKQRMDRR
          QQVKDVQKLRKKELKTLLPHDPTA.VFV.PA.EKPIEIQWVKPEPKVDLKARKKRIYKRQRKMKQRMDRR
Retrocopy QQVKDVQKLRKKELKTLLPHDPTAGVFVMPAEEKPIEIQWVKPEPKVDLKARKKRIYKRQRKMKQRMDRR

Parental  KTK
          KTK
Retrocopy KTK

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	0.07 RPM	9.30 RPM
SRP051959_heart	0.02 RPM	11.47 RPM
SRP051959_kidney	0.07 RPM	14.80 RPM
SRP051959_liver	0.00 RPM	11.33 RPM
SRP051959_lung	0.05 RPM	15.37 RPM
SRP051959_lymph_node	0.16 RPM	16.32 RPM
SRP051959_skeletal_muscle	0.07 RPM	12.21 RPM
SRP051959_spleen	0.08 RPM	14.41 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1389 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1389 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001790	2 retrocopies	retro_chof_1664, retro_chof_1776,
Callithrix jacchus	ENSCJAG00000018506	1 retrocopy	retro_cjac_1389 ,
Homo sapiens	ENSG00000113460	1 retrocopy	retro_hsap_3954,
Gorilla gorilla	ENSGGOG00000004225	1 retrocopy	retro_ggor_2657,
Loxodonta africana	ENSLAFG00000007249	1 retrocopy	retro_lafr_1116,
Myotis lucifugus	ENSMLUG00000029255	3 retrocopies	retro_mluc_1402, retro_mluc_707, retro_mluc_963,
Macaca mulatta	ENSMMUG00000000442	1 retrocopy	retro_mmul_2289,
Monodelphis domestica	ENSMODG00000020386	1 retrocopy	retro_mdom_1032,
Nomascus leucogenys	ENSNLEG00000014452	1 retrocopy	retro_nleu_533,
Otolemur garnettii	ENSOGAG00000014827	2 retrocopies	retro_ogar_3116, retro_ogar_793,
Pongo abelii	ENSPPYG00000015390	2 retrocopies	retro_pabe_3258, retro_pabe_3379,
Pan troglodytes	ENSPTRG00000016784	1 retrocopy	retro_ptro_2684,
Rattus norvegicus	ENSRNOG00000018021	1 retrocopy	retro_rnor_1140,
Tupaia belangeri	ENSTBEG00000011652	9 retrocopies	retro_tbel_1963, retro_tbel_1964, retro_tbel_2981, retro_tbel_3002, retro_tbel_3082, retro_tbel_4194, retro_tbel_4229, retro_tbel_4418, retro_tbel_954,