RetrogeneDB ID: retro_cjac_1234

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:83494054..83495358(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000008113
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3L
• Ensembl ID: ENSCJAG00000012225
• Aliases: None
• Description: None

Sequence

>retro_cjac_1234
CAGGTGATCCCTGAGGTGATCAAGAACTTCATGCCAATATTTCCACAAAACTGTCTCAGATTTGATTGACCAGAAAGTGT
ATGAGCTACAGGCCAGTCGAGTCTCCAGCAATGTCATTGACCAGAAGGTATATGAGATCCAGAACATCTATGAGAACAAG
CTGACTGAAAGATTCTTCAAGAATACACCTTGGCCGGAGGCTGAAGCCATTGCTCCACAGGTTGGCAACGATGCTGTCTT
CCTGATTTTATACAAAGAATTATACTACAGGCACATATATGCCAAAGTCAGTGGGGGACGTTCCTTGGAGCAGAGGTTTG
AATCCTATTACAACTATTGCAATCTCTTCAACTACATTCTTAATGCTGATGGTCCTGCTCCCCTTGAACTACCCAACCAG
TGGCTCTGGGATATCATCGATGAGTTCATCTACTGGTTTCAGTCATTCAGTCAGTTACCGGTGCAAGACTGCCAAGAAGT
CAGAGGAGGAGATTGACTTCCTTCGTTCCAATCCCAAAATCTGGAATGTTCACAATGTCCTCAATGTCCTTCATTGCCTA
GTAGACAAATCCAACATCAACCGACAGTTGGAGGTATACACAAGCGGAGGTGACCCTGAGAGTGTGGCTGGGTAGTATGG
GCGGCACTCCCTCTACAAGATGCTTGGTCACTTCAGCCTGGTGGGGCTTCTCTGCCTGCACTCCCTGTTAGGAGATTACT
ACCAGGCCATCAAGGTGCTGGAGAACATCAAACTGAACAAAAAGAGTATGTATTCCCGTGTTCCAGAGTGCCAGGTCACC
ACGTACTATTATGTTGGATTTGCATATTTGATGATGCGTCGCTACCAGGATGCCATCTGGGTCTTTGCCAACGTCCTCCT
CTACATCCGGAGGACCAAAGGCATGTTCCAGAGGACCACATATAAGTATGAGATGATTATCAAACAGAATGAGCAGATGC
ATGCGCTGCTGGCTATTGCCCTCACCATGTACCCCATGCATATCGATGAGAGCATTCACCTCCAACTGCGGGAGAAATAT
GGGGACAGCATGCTGCTCATGCAGAAAGGTGACCCACAAGTCTATGAAGAACCTTTCAGTTACTCCTGCCCCAAGTTTCT
ATCACCAGTAGTGCCCAACTATGATAATGTGCACCCCAACTACCACAAAGAGCCCTTCCTGCAGCAGCTGAATGTGTTTG
CTGATAAAGTACAGCAGCAGGCCCAGCTTTCAACCATCCGCAGCTTCCTCAAGCTCTATACCACCATGCCTGTAGCCAAG
CTGGCTGGCTTCCTGGATCTCACA

Alignment

ORF - retro_cjac_1234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.85 %
• Parental protein coverage: 71.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVIPEVIKNFI-QYFHKTVSDLIDQKVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPE
          QVIPEVIKNF..QYFHKTVSDLIDQKVYELQASRVSS.VIDQKVYEIQ.IYEN...KLTERFFKNTPWPE
Retrocopy QVIPEVIKNFM>QYFHKTVSDLIDQKVYELQASRVSSNVIDQKVYEIQNIYEN---KLTERFFKNTPWPE

Parental  AEAIAPQVGNDAVFLILYKELYYRHIYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLW
          AEAIAPQVGNDAVFLILYKELYYRHIYAKVSGG.SLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLW
Retrocopy AEAIAPQVGNDAVFLILYKELYYRHIYAKVSGGRSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLW

Parental  DIIDEFIYQFQSFSQ-YRCKTAKKSEEEIDFLRSNPKIWNVHSVLNVLHSLVDKSNINRQLEVYTSGGDP
          DIIDEFIY.FQSFSQ.YRCKTAKKSEEEIDFLRSNPKIWNVH.VLNVLH.LVDKSNINRQLEVYTSGGDP
Retrocopy DIIDEFIYWFQSFSQ>YRCKTAKKSEEEIDFLRSNPKIWNVHNVLNVLHCLVDKSNINRQLEVYTSGGDP

Parental  ESVAGEYGRHSLYKMLGYFSLVGLLRLHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAY
          ESVAG.YGRHSLYKMLG.FSLVGLL.LHSLLGDYYQAIKVLENI.LNKKSMYSRVPECQVTTYYYVGFAY
Retrocopy ESVAG*YGRHSLYKMLGHFSLVGLLCLHSLLGDYYQAIKVLENIKLNKKSMYSRVPECQVTTYYYVGFAY

Parental  LMMRRYQDAIRVFANILLYIQRTKSMFQRTTYKYEMINKQNEQMHALLAIALTMYPMRIDESIHLQLREK
          LMMRRYQDAI.VFAN.LLYI.RTK.MFQRTTYKYEMI.KQNEQMHALLAIALTMYPM.IDESIHLQLREK
Retrocopy LMMRRYQDAIWVFANVLLYIRRTKGMFQRTTYKYEMIIKQNEQMHALLAIALTMYPMHIDESIHLQLREK

Parental  YGDKMLRMQKGDPQVYEELFSYSCPKFLSPVVPNYDNVHPNYHKEPFLQQLKVFADEVQQQAQLSTIRSF
          YGD.ML.MQKGDPQVYEE.FSYSCPKFLSPVVPNYDNVHPNYHKEPFLQQL.VFAD.VQQQAQLSTIRSF
Retrocopy YGDSMLLMQKGDPQVYEEPFSYSCPKFLSPVVPNYDNVHPNYHKEPFLQQLNVFADKVQQQAQLSTIRSF

Parental  LKLYTTMPVAKLAGFLDLT
          LKLYTTMPVAKLAGFLDLT
Retrocopy LKLYTTMPVAKLAGFLDLT

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	0.09 RPM	108.45 RPM
SRP051959_heart	0.16 RPM	86.60 RPM
SRP051959_kidney	0.22 RPM	97.97 RPM
SRP051959_liver	0.04 RPM	113.18 RPM
SRP051959_lung	0.08 RPM	115.16 RPM
SRP051959_lymph_node	0.14 RPM	144.26 RPM
SRP051959_skeletal_muscle	0.04 RPM	93.25 RPM
SRP051959_spleen	0.13 RPM	133.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1234 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1234 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1234 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012225	1 retrocopy	retro_cjac_1234 ,
Monodelphis domestica	ENSMODG00000019068	3 retrocopies	retro_mdom_1247, retro_mdom_1585, retro_mdom_432,
Otolemur garnettii	ENSOGAG00000029444	1 retrocopy	retro_ogar_1635,
Pan troglodytes	ENSPTRG00000014352	1 retrocopy	retro_ptro_940,