RetrogeneDB ID: retro_mmus_3963

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: Y:1268547..1268885(-)
• Located in intron of: ENSMUSG00000069045

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif1
• Ensembl ID: ENSMUSG00000035530
• Aliases: Eif1, Sui1-rs1
• Description: eukaryotic translation initiation factor 1 [Source:MGI Symbol;Acc:MGI:105125]

Sequence

>retro_mmus_3963
ATGTCCACTATCCTGAACCTCAACTCTTTCGACCCCTTTGCTGATGCAAGTAAGGGTGATGACATGCTTCCTGCTGGCAC
TGAGGATTATATCCATGTAAGAATTCAACAGAGAAACGGCAGGAAGACCCTTACAACTGTCCAAGGGATCACTGATGAAT
ACGATTAAAAGAAACTAGTGAAGGCGTTTAAGAAGAAATTTGCCTGCAATGGTACTGTAATTGAGCATCCAGAATATAGA
GAAGTAATTCAGGTACAGGGTGATAGTGTAAGAACATACACCAGTTCCTGATAGAGATTGGACTGGCTAAGGATGATCAG
CTGATGGTTCATGGGTTT

Alignment

ORF - retro_mmus_3963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKFACN
          MS.I.NL.SFDPFADASKGDD.LPAGTEDYIH.RIQQRNGRKTLTTVQGI.D.YD.KKLVKAFKKKFACN
Retrocopy MSTILNLNSFDPFADASKGDDMLPAGTEDYIHVRIQQRNGRKTLTTVQGITDEYD*KKLVKAFKKKFACN

Parental  GTVIEHPEYGEVIQLQGDQ-RKNICQFLIEIGLAKDDQLKVHGF
          GTVIEHPEY.EVIQ.QGD...KNI.QFLIEIGLAKDDQL.VHGF
Retrocopy GTVIEHPEYREVIQVQGDS<CKNIHQFLIEIGLAKDDQLMVHGF

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	0.16 RPM	129.24 RPM
SRP007412_cerebellum	0.30 RPM	91.10 RPM
SRP007412_heart	0.09 RPM	194.38 RPM
SRP007412_kidney	0.29 RPM	123.04 RPM
SRP007412_liver	0.16 RPM	113.49 RPM
SRP007412_testis	0.09 RPM	149.52 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_3963 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	Y:1269613..1269933
ENCFF001YKA	POLR2A	Y:1268768..1268797

EST

No EST(s) were mapped for retro_mmus_3963 retrocopy.

TSS

No TSS is located nearby retro_mmus_3963 retrocopy 5' end.

Lab

retro_mmus_3963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3963 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002282	1 retrocopy	retro_btau_63,
Callithrix jacchus	ENSCJAG00000012120	6 retrocopies	retro_cjac_1237, retro_cjac_2089, retro_cjac_346, retro_cjac_3815, retro_cjac_600, retro_cjac_84,
Cavia porcellus	ENSCPOG00000014350	3 retrocopies	retro_cpor_42, retro_cpor_613, retro_cpor_643,
Felis catus	ENSFCAG00000024455	2 retrocopies	retro_fcat_1555, retro_fcat_74,
Myotis lucifugus	ENSMLUG00000005077	3 retrocopies	retro_mluc_233, retro_mluc_305, retro_mluc_330,
Mustela putorius furo	ENSMPUG00000010883	6 retrocopies	retro_mputfur_1019, retro_mputfur_1072, retro_mputfur_1239, retro_mputfur_1299, retro_mputfur_41, retro_mputfur_752,
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,
Nomascus leucogenys	ENSNLEG00000011013	3 retrocopies	retro_nleu_1482, retro_nleu_2005, retro_nleu_92,
Pongo abelii	ENSPPYG00000029667	1 retrocopy	retro_pabe_127,
Rattus norvegicus	ENSRNOG00000032769	1 retrocopy	retro_rnor_520,
Rattus norvegicus	ENSRNOG00000033765	15 retrocopies	retro_rnor_1088, retro_rnor_1347, retro_rnor_1518, retro_rnor_1744, retro_rnor_1971, retro_rnor_2067, retro_rnor_2171, retro_rnor_2203, retro_rnor_2532, retro_rnor_2548, retro_rnor_2579, retro_rnor_45, retro_rnor_532, retro_rnor_571, retro_rnor_65,
Sarcophilus harrisii	ENSSHAG00000005729	1 retrocopy	retro_shar_42,