RetrogeneDB ID: retro_mmus_587

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:91228185..91228512(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif1b
• Ensembl ID: ENSMUSG00000006941
• Aliases: Eif1b, 1500010M16Rik, 3110001N14Rik, Gc20
• Description: eukaryotic translation initiation factor 1B [Source:MGI Symbol;Acc:MGI:1916219]

Sequence

>retro_mmus_587
ATGCCCACTGTCCAGAACTTCCAATCTTTCGACCCCCTTGCTGATGCAACTAAGGGCAATGACTTACTCCCCGCAGGGAC
TGAGGACTACATTCATATAAGAATCCAGCAGCGGGACGGCAGGCAGACCCTGATCGCTGTGCAGGGTGTTGCGGACAGTT
ATGACAAAAAGAAACTTGTGAAAGCTTTCAGGAAGAAACCTGCCTGTAATGGACGTGTGATTGACCATCCCAAGTACAGA
GAGGTTACTCAGCTTCAAGGTGACCAAAGGAAGAGCGTTTGCCAGTTTCTTTTGGAGGCTGGCATCACCAAGGCGGTTCA
CGGATTC

Alignment

ORF - retro_mmus_587 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTIQNLQSFDPFADATKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACN
          M.T.QN.QSFDP.ADATKG.DLLPAGTEDYIHIRIQQR.GR.TL..VQG.AD.YDKKKLVKAF.KK.ACN
Retrocopy MPTVQNFQSFDPLADATKGNDLLPAGTEDYIHIRIQQRDGRQTLIAVQGVADSYDKKKLVKAFRKKPACN

Parental  GTVIEHPEYGEVIQLQGDQRKNICQFLLEVGIVKEEQLKVHGF
          G.VI.HP.Y.EV.QLQGDQRK..CQFLLE.GI.K.....VHGF
Retrocopy GRVIDHPKYREVTQLQGDQRKSVCQFLLEAGITK----AVHGF

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
SRP007412_brain	0.00 RPM	61.63 RPM
SRP007412_cerebellum	0.00 RPM	83.33 RPM
SRP007412_heart	0.00 RPM	34.52 RPM
SRP007412_kidney	0.00 RPM	35.02 RPM
SRP007412_liver	0.00 RPM	16.63 RPM
SRP007412_testis	0.00 RPM	122.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_587 was not detected

EST

No EST(s) were mapped for retro_mmus_587 retrocopy.

TSS

No TSS is located nearby retro_mmus_587 retrocopy 5' end.

Lab

retro_mmus_587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_587 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013689	4 retrocopies	retro_dord_179, retro_dord_307, retro_dord_626, retro_dord_669,
Echinops telfairi	ENSETEG00000017295	5 retrocopies	retro_etel_1228, retro_etel_1480, retro_etel_1793, retro_etel_31, retro_etel_4,
Microcebus murinus	ENSMICG00000013223	5 retrocopies	retro_mmur_254, retro_mmur_445, retro_mmur_535, retro_mmur_654, retro_mmur_706,
Macaca mulatta	ENSMMUG00000017704	1 retrocopy	retro_mmul_154,
Monodelphis domestica	ENSMODG00000011056	2 retrocopies	retro_mdom_1113, retro_mdom_1382,
Mus musculus	ENSMUSG00000006941	1 retrocopy	retro_mmus_587 ,
Mus musculus	ENSMUSG00000035530	27 retrocopies	retro_mmus_1033, retro_mmus_1063, retro_mmus_1191, retro_mmus_1213, retro_mmus_1286, retro_mmus_1392, retro_mmus_1448, retro_mmus_1652, retro_mmus_2045, retro_mmus_2270, retro_mmus_2604, retro_mmus_2737, retro_mmus_2990, retro_mmus_3043, retro_mmus_3047, retro_mmus_308, retro_mmus_3141, retro_mmus_3164, retro_mmus_3386, retro_mmus_3468, retro_mmus_3471, retro_mmus_3638, retro_mmus_3639, retro_mmus_3963, retro_mmus_512, retro_mmus_585, retro_mmus_840,
Otolemur garnettii	ENSOGAG00000025224	1 retrocopy	retro_ogar_1943,
Ictidomys tridecemlineatus	ENSSTOG00000012168	1 retrocopy	retro_itri_1597,
Tupaia belangeri	ENSTBEG00000013185	6 retrocopies	retro_tbel_1861, retro_tbel_1920, retro_tbel_1996, retro_tbel_2954, retro_tbel_3209, retro_tbel_3867,
Tarsius syrichta	ENSTSYG00000006338	3 retrocopies	retro_tsyr_1574, retro_tsyr_2154, retro_tsyr_888,