RetrogeneDB ID: retro_cjac_2556

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:110070555..110071038(+)
• Located in intron of: ENSCJAG00000007985

Retrocopy information

• Ensembl ID: ENSCJAG00000008071
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAX
• Ensembl ID: ENSCJAG00000019702
• Aliases: None
• Description: MYC associated factor X [Source:HGNC Symbol;Acc:6913]

Sequence

>retro_cjac_2556
ATGAGCGATAACGATGACATCAAGGTGGAGAGCGACGAAGAGCAACCGAGGTTTCAATCTGCGGCTGACAAACGGGCTCA
TCATAATGCACTGGAACGAAAACGTAGGGACCACATCAAAGACAGCTTTCACAGTTTGCGGGACTCAGACCCATCACTCC
AAGGAGAGAAGCCACAGGCATCCTGGGCCCAAATCCTAGACAAAGCCACAGAGTATATCCAGTATATGCGAAGGAAAAAC
CACACACACCAGCAAGATATTGACGACCTCAAGCAGCAGAATGCTCTTCTGGAGCAGCAGGTCCGTGCACTGGAGAAGGT
GAGGTCAAGTGCCCAACTGCAGACCAACTACCCCGCCTCAGACAGCAGCCTCTACACCAACGCCAAGGGCAGCACCATCT
CTGCCTTCGATGGGGGCTCAGACTCCAGCTTAGAGTCTGAGCCTGAAGAGCCCCAAAGCAGGAAGAAGCTCCGGATGGAG
GCC

Alignment

ORF - retro_cjac_2556 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.79 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDNDDIEVESDEEQPRFQSAADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEK--ASRAQILDKAT
          MSDNDDI.VESDEEQPRFQSAADKRAHHNALERKRRDHIKDSFHSLRDS.PSLQGEK..AS.AQILDKAT
Retrocopy MSDNDDIKVESDEEQPRFQSAADKRAHHNALERKRRDHIKDSFHSLRDSDPSLQGEKPQASWAQILDKAT

Parental  EYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRALEKARSSAQLQTNYPSSDNSLYTNAKGSTISAFDGGS
          EYIQYMRRKNHTHQQDIDDLK.QNALLEQQVRALEK.RSSAQLQTNYP.SD.SLYTNAKGSTISAFDGGS
Retrocopy EYIQYMRRKNHTHQQDIDDLKQQNALLEQQVRALEKVRSSAQLQTNYPASDSSLYTNAKGSTISAFDGGS

Parental  DSSSESEPEEPQSRKKLRMEA
          DSS.ESEPEEPQSRKKLRMEA
Retrocopy DSSLESEPEEPQSRKKLRMEA

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	0.67 RPM	8.48 RPM
SRP051959_heart	0.44 RPM	7.10 RPM
SRP051959_kidney	0.51 RPM	8.48 RPM
SRP051959_liver	0.28 RPM	7.21 RPM
SRP051959_lung	0.88 RPM	14.62 RPM
SRP051959_lymph_node	0.37 RPM	16.07 RPM
SRP051959_skeletal_muscle	0.22 RPM	5.92 RPM
SRP051959_spleen	0.53 RPM	13.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2556 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2556 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003472	2 retrocopies	retro_amel_1261, retro_amel_1606,
Canis familiaris	ENSCAFG00000016212	2 retrocopies	retro_cfam_1179, retro_cfam_1325,
Callithrix jacchus	ENSCJAG00000019702	2 retrocopies	retro_cjac_2057, retro_cjac_2556 ,
Cavia porcellus	ENSCPOG00000010172	1 retrocopy	retro_cpor_710,
Erinaceus europaeus	ENSEEUG00000003973	3 retrocopies	retro_eeur_216, retro_eeur_344, retro_eeur_37,
Echinops telfairi	ENSETEG00000002967	1 retrocopy	retro_etel_1294,
Felis catus	ENSFCAG00000010347	1 retrocopy	retro_fcat_278,
Macaca mulatta	ENSMMUG00000004341	1 retrocopy	retro_mmul_1648,
Mustela putorius furo	ENSMPUG00000006859	3 retrocopies	retro_mputfur_1218, retro_mputfur_1615, retro_mputfur_192,
Mus musculus	ENSMUSG00000059436	8 retrocopies	retro_mmus_2891, retro_mmus_2892, retro_mmus_2893, retro_mmus_2894, retro_mmus_2991, retro_mmus_2992, retro_mmus_2993, retro_mmus_2994,
Nomascus leucogenys	ENSNLEG00000014373	1 retrocopy	retro_nleu_1122,
Ochotona princeps	ENSOPRG00000016245	1 retrocopy	retro_opri_945,
Pongo abelii	ENSPPYG00000005911	1 retrocopy	retro_pabe_3097,
Rattus norvegicus	ENSRNOG00000008049	3 retrocopies	retro_rnor_1653, retro_rnor_1877, retro_rnor_2369,
Ictidomys tridecemlineatus	ENSSTOG00000028142	1 retrocopy	retro_itri_42,
Tupaia belangeri	ENSTBEG00000012645	1 retrocopy	retro_tbel_3407,