RetrogeneDB ID: retro_cjac_3203

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:29473539..29474321(+)
• 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_3203
GGTTTTGAGAAGCCTTCTGCCATCCAGCAGCGAGCCATTCTACCTTGTATCAAGGGTTATGATGTGATCGCTCAAGCCCA
ATTTGGGACTGGGAAAATGGCCACATTTGCCATATCGATTTTGCAGCAGATTGAATTAGATCTAAAGGCCACCCAGGCCT
TGGTTCTAGCACTCACTTGAGAATTGACCCAGCAGGTACAGAAGGTGGTCATGGCACTAGGAGACTACATGGGTGCCTCC
TATCACGCCTGTACTGGGGGGCACCAACATGCGTGCTGAGGTGCAAAACTGCAGATGGAAGCTCCCCATATCATTGTAGG
AACCCCTGGCCATGTGTTCGATATGTTTAATCGGAGATACTTGTCTCCCAAATACATCAAGATGTTTGTATTGGACGAAG
CTGATGAAATGTTAAGCCGTGGATTCAAGGACCAGATATATGACATATTCCAAAAGCTCAACAGCAGCACCCAGGTAGTT
TTGTTGTCAGCTACGATGCCTTCTCATGTGCTTGAGGTGACTAAGAAGTTCATGAGGGACCCCATTCGGATTCTTGTCAA
GAAGGAAGAGTATCTGCCCTGGAGGGTATCTGCCAATTCAACATCAACATGGAATGAGAGGAGTGGAAGCTGGACACACT
GTATGACTTGTATGAAACCCTGATCATCACTCAGGCAGTCATCTTCATTAACACCCGAAGGAAGGTGGACTGGCTCACTG
AGAAGATAAATGCTCGATATTTCACTGTCTCTGCCATGCATGGAGATGTGATCATGAGGGAG

Alignment

ORF - retro_cjac_3203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 64.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQAQIQK
          GFEKPSAIQQRAILPCIKGYDVIAQAQ.GTGK.ATFAISILQQIELDLKATQALVLA.T.EL.QQ...QK
Retrocopy GFEKPSAIQQRAILPCIKGYDVIAQAQFGTGKMATFAISILQQIELDLKATQALVLALT*ELTQQ--VQK

Parental  VVMALGDYMGASCHAC-IGGTNVRAEVQ-KLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADE
          VVMALGDYMGAS.HAC..GGTN.RAEVQ.KLQMEAPHIIVGTPG.VFDM.NRRYLSPKYIKMFVLDEADE
Retrocopy VVMALGDYMGASYHAC>LGGTNMRAEVQ<KLQMEAPHIIVGTPGHVFDMFNRRYLSPKYIKMFVLDEADE

Parental  MLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK-KEEL-TLEGIRQFYINVE
          MLSRGFKDQIYDIFQKLNS.TQVVLLSATMPS.VLEVTKKFMRDPIRILVK..E.L..LEGI.QF.IN.E
Retrocopy MLSRGFKDQIYDIFQKLNSSTQVVLLSATMPSHVLEVTKKFMRDPIRILVKKEEYL<ALEGICQFNINME

Parental  REEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKE
          .EEWKLDTL.DLYETL.ITQAVIFINTRRKVDWLTEK..AR.FTVSAMHGD....E
Retrocopy *EEWKLDTLYDLYETLIITQAVIFINTRRKVDWLTEKINARYFTVSAMHGDVIMRE

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	0.00 RPM	66.55 RPM
SRP051959_kidney	0.02 RPM	99.26 RPM
SRP051959_liver	0.02 RPM	195.66 RPM
SRP051959_lung	0.00 RPM	100.79 RPM
SRP051959_lymph_node	0.05 RPM	96.91 RPM
SRP051959_skeletal_muscle	0.02 RPM	69.60 RPM
SRP051959_spleen	0.00 RPM	103.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3203 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3203 has 0 orthologous retrocopies within eutheria group .

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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,