RetrogeneDB ID: retro_cjac_395

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:54337648..54338256(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSCJAG00000015114
• Aliases: None
• Description: eukaryotic initiation factor 4A-I [Source:RefSeq peptide;Acc:NP_001192066]

Sequence

>retro_cjac_395
GACATGAACCTCCCAAATTCCCTCCTTCATGGCATCTATGCTTATGGTTTTGAGAAGCCCTCTGCTATAGCCATTCTACC
TTGTGTCAAAGGTTATGACGTGATCGCTGAAGCCCAATATGGGACTGGGAAAACGGCCTCATTTGCTATATTGATTCTGC
AGCAGTCTGAATTAGATCTAAAGGCTAACCAGGCCTTGGTCCTAGCACCCACTCAAGAATCAGCTCAGCAGATACAGAAG
GTGGTCATAGCACTAGGATACTACATAGGTGCCTCCTGTCACGCCTGTGTTGAGGGCACCAACGTACATGCTCAGGTGTA
GAAACAGCAGATGAAAGCTCCCTGTATCATTGTGGATACCCTGGCCATGTGTTTGATATGCTTAACAGGAAATACCTGTC
TCCCAAATACATCAAGATGTTTGTACTGGACATAGCTGACAAAATGTTAAGTCATGGATTCAAGGACCAGATCAATGACA
TATTCCCAAAGCTCAACAGCAACACCCAGGTAGTTTTGCTGTCAGCTACAATGCCTTCTAATATGCCTGAGGTGACCAAG
AAGTTCATGAGGGACTCGATTTGGATTCTTGTCAAGAAGAGTCGAATC

Alignment

ORF - retro_cjac_395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.47 %
• Parental protein coverage: 50.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALV
          DMNL..SLL.GIYAYGFEKPSAI...AILPC.KGYDVIA.AQ.GTGKTA.FAI.ILQQ.ELDLKA.QALV
Retrocopy DMNLPNSLLHGIYAYGFEKPSAI---AILPCVKGYDVIAEAQYGTGKTASFAILILQQSELDLKANQALV

Parental  LAPTRELAQQAQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGT-PGRVFDMLNRRYLS
          LAPT.E.AQQ..IQKVV.ALG.Y.GASCHAC..GTNV.A.V.K.QM.AP.IIV.T.PG.VFDMLNR.YLS
Retrocopy LAPTQESAQQ--IQKVVIALGYYIGASCHACVEGTNVHAQV*KQQMKAPCIIVDT<PGHVFDMLNRKYLS

Parental  PKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEEL
          PKYIKMFVLD.AD.MLS.GFKDQI.DIF.KLNSNTQVVLLSATMPS...EVTKKFMRD.I.ILVKK...
Retrocopy PKYIKMFVLDIADKMLSHGFKDQINDIFPKLNSNTQVVLLSATMPSNMPEVTKKFMRDSIWILVKKSRI

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	0.00 RPM	121.41 RPM
SRP051959_heart	0.04 RPM	66.55 RPM
SRP051959_kidney	0.00 RPM	99.26 RPM
SRP051959_liver	0.00 RPM	195.66 RPM
SRP051959_lung	0.07 RPM	100.79 RPM
SRP051959_lymph_node	0.02 RPM	96.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	69.60 RPM
SRP051959_spleen	0.02 RPM	103.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_395 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_395 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_395 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1270
Pan troglodytes	retro_ptro_870
Gorilla gorilla	retro_ggor_998

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016753	1 retrocopy	retro_amel_1300,
Callithrix jacchus	ENSCJAG00000015114	8 retrocopies	retro_cjac_1876, retro_cjac_2046, retro_cjac_2521, retro_cjac_2679, retro_cjac_3086, retro_cjac_3203, retro_cjac_395 , retro_cjac_727,
Dipodomys ordii	ENSDORG00000014225	1 retrocopy	retro_dord_732,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Microcebus murinus	ENSMICG00000014759	2 retrocopies	retro_mmur_1164, retro_mmur_1477,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Otolemur garnettii	ENSOGAG00000008132	2 retrocopies	retro_ogar_1375, retro_ogar_1862,
Ochotona princeps	ENSOPRG00000008591	2 retrocopies	retro_opri_155, retro_opri_985,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,