RetrogeneDB ID: retro_cjac_2333

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:44745983..44747316(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000005440
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3E
• Ensembl ID: ENSCJAG00000006458
• Aliases: None
• Description: Eukaryotic translation initiation factor 3 subunit E [Source:UniProtKB/TrEMBL;Acc:F6RU74]

Sequence

>retro_cjac_2333
ATGGCGGAGTACGACTTAACTACTCACATCACGCACTTTCTGGATCGGCATCTAGTCTTTCCGCTTTTGGAGTTTCTCTC
TGTAAAGGAGATATATAATGAAAAGGAATTATTACAAGGTAAATTGGACCTTCTTAGTGATACCAACATGGTAGACTTTG
CTATGGATGTTTACAAAAACCTTTATTCTGATGATATTCCTCATGCTTTGAGAGAGAAAAGAACCACAGTTGTTGCACAA
CTGAAACAGCTTCAGGCAGAAACAGAACCAATTGTGAAGATGTTTGAAGATCCAGAAACTACAAGGCAAATGCAGTCAAC
CAGGATGGTAGGATGCTCTTTGACTACCTGGCGGACAAACATGGTTTTAGGCAGGAATATTTAGACACCCTCTACAGATA
TGCAAAATTCCAATATGAATGTGGGAATTACTCAGGAGCAGCAGAATATCTTTATTTTTTTAGAGTGTTGGTTCCAGCAA
CAGATAGAAATGCATTAAGTTCACTCTGGGGAAAGCTGGCCTCTGAAATCTTAATGCAGAATTGGGATGCCACCATGGAA
GATCTTACACGGTTAAAAGAGACCATAGATAATAATTCTGTGAGTTCTCCACTCCAGTCTCTTCAGCAGAGAACATGGCT
TATTCACTGGTCCCTGTTTGTTTTCTTCAATCACCCCAAAGTTCGCGATAATATTATCGATCTCTTCTTTACCAGCCACA
GTATCTTAATGCAATTCAGACAATGTGTCCACACATTCTTCGCTATTTGACTACAGCAGTCATAACAAACAAGGATGTTC
GAAAACGCCGGCAAGTGCTGAAAGATCTAGTTAAGATTATTCAACAGGAGTCTCACACATATAAGGACCCAATTACAGAA
TTTGTTGAATGCTTATATGTTAACTTTGACTTTGATGGGGCTCAGAAAAAGCTGAGGGAATGTGAATCAGTGCTTGTGAA
TGACTTCTTCTTGGTGGCCTGTCTTGAAGATTTCATTGAAAATGCCCGTCTCTTCATATTTGAAACTTTCTGTCACATCC
ACCAGTGTATCAGCATTAACATGTTGGCGGATAAACTGAACGTGACTCCAGAAGAAGCTGAAAGGTGGATTGTAAATTTG
ATTAGAAATGCAAGACTGGATGCCAAGATTGATTCTAAATTGGGTCATGTGGTTATGGGTAACAATGCAGTCTCACCCTA
TCAGCAAGTGATTGAAAAGACCAAAAGCCTTTCTTTTAGAAGCCAGATGTTGGCCATGAATATTGAGAAGAAACTTAATC
AGAATAGCAGGTCAGAGGCTCCTAACTGGGCAACTCAAGATTCTGGATTCTAC

Alignment

ORF - retro_cjac_2333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEYDLTTRIAHFLDRHLVFPLLEFLSVKEIYNEKELLQGKLDLLSDTNMVDFAMDVYKNLYSDDIPHAL
          MAEYDLTT.I.HFLDRHLVFPLLEFLSVKEIYNEKELLQGKLDLLSDTNMVDFAMDVYKNLYSDDIPHAL
Retrocopy MAEYDLTTHITHFLDRHLVFPLLEFLSVKEIYNEKELLQGKLDLLSDTNMVDFAMDVYKNLYSDDIPHAL

Parental  REKRTTVVAQLKQLQAETEPIVKMFEDPETTRQMQSTR-DGRMLFDYLADKHGFRQEYLDTLYRYAKFQY
          REKRTTVVAQLKQLQAETEPIVKMFEDPETTRQMQSTR.DGRMLFDYLADKHGFRQEYLDTLYRYAKFQY
Retrocopy REKRTTVVAQLKQLQAETEPIVKMFEDPETTRQMQSTR<DGRMLFDYLADKHGFRQEYLDTLYRYAKFQY

Parental  ECGNYSGAAEYLYFFRVLVPATDRNALSSLWGKLASEILMQNWDAAMEDLTRLKETIDNNSVSSPLQSLQ
          ECGNYSGAAEYLYFFRVLVPATDRNALSSLWGKLASEILMQNWDA.MEDLTRLKETIDNNSVSSPLQSLQ
Retrocopy ECGNYSGAAEYLYFFRVLVPATDRNALSSLWGKLASEILMQNWDATMEDLTRLKETIDNNSVSSPLQSLQ

Parental  QRTWLIHWSLFVFFNHPKGRDNIIDLF-LYQPQYLNAIQTMCPHILRYLTTAVITNKDVRKRRQVLKDLV
          QRTWLIHWSLFVFFNHPK.RDNIIDLF.LYQPQYLNAIQTMCPHILRYLTTAVITNKDVRKRRQVLKDLV
Retrocopy QRTWLIHWSLFVFFNHPKVRDNIIDLF<LYQPQYLNAIQTMCPHILRYLTTAVITNKDVRKRRQVLKDLV

Parental  KVIQQESYTYKDPITEFVECLYVNFDFDGAQKKLRECESVLVNDFFLVACLEDFIENARLFIFETFCRIH
          K.IQQES.TYKDPITEFVECLYVNFDFDGAQKKLRECESVLVNDFFLVACLEDFIENARLFIFETFC.IH
Retrocopy KIIQQESHTYKDPITEFVECLYVNFDFDGAQKKLRECESVLVNDFFLVACLEDFIENARLFIFETFCHIH

Parental  QCISINMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQML
          QCISINMLADKLN.TPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQML
Retrocopy QCISINMLADKLNVTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQML

Parental  AMNIEKKLNQNSRSEAPNWATQDSGFY
          AMNIEKKLNQNSRSEAPNWATQDSGFY
Retrocopy AMNIEKKLNQNSRSEAPNWATQDSGFY

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	0.27 RPM	72.49 RPM
SRP051959_heart	0.21 RPM	85.05 RPM
SRP051959_kidney	0.16 RPM	77.47 RPM
SRP051959_liver	0.28 RPM	111.94 RPM
SRP051959_lung	0.28 RPM	97.67 RPM
SRP051959_lymph_node	0.30 RPM	137.12 RPM
SRP051959_skeletal_muscle	0.39 RPM	134.76 RPM
SRP051959_spleen	0.40 RPM	138.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2333 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2333 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333 , retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,