RetrogeneDB ID: retro_mmus_150

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:49945095..49945335(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094886
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ier3ip1
• Ensembl ID: ENSMUSG00000090000
• Aliases: Ier3ip1, 1110057H19Rik, AI644142, AL022842, AL022863, AV026606
• Description: immediate early response 3 interacting protein 1 [Source:MGI Symbol;Acc:MGI:1913441]

Sequence

>retro_mmus_150
ATGGCCTTCACGCTGTACTCCCTGATGCAAGCGGCCCTGCTGTGCATCTCTGTGCTGCAGGAGGAGCACTTCCTCAAGAA
CATTGGCTGGGGAACAGACCAGGGAATTAGTGGATTCGGAGAGGAGTCAGGAATTAAATCTCAACTAATGAACCTTATTC
GGTCTGTGAGAACCGTGATGAGAGTGCCATTGACAATAGTAAGCTCAATTACTATTGTATTGCTTCTGTTATTTGGCTAA

Alignment

ORF - retro_mmus_150 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFTLYSLMQAALLCVNAIAVLHEERFLKNIGWGTDQGIGGFGEEPGIKSQLMNLIRSVRTVMRVPLIIV
          MAFTLYSLMQAALLC...I.VL.EE.FLKNIGWGTDQGI.GFGEE.GIKSQLMNLIRSVRTVMRVPL.IV
Retrocopy MAFTLYSLMQAALLC---ISVLQEEHFLKNIGWGTDQGISGFGEESGIKSQLMNLIRSVRTVMRVPLTIV

Parental  NSITIVLLLLFG
          .SITIVLLLLFG
Retrocopy SSITIVLLLLFG

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	0.02 RPM	17.92 RPM
SRP007412_cerebellum	0.00 RPM	11.94 RPM
SRP007412_heart	0.00 RPM	9.49 RPM
SRP007412_kidney	0.02 RPM	11.26 RPM
SRP007412_liver	0.00 RPM	4.72 RPM
SRP007412_testis	0.00 RPM	10.66 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_150 was not detected

EST

No EST(s) were mapped for retro_mmus_150 retrocopy.

TSS

No TSS is located nearby retro_mmus_150 retrocopy 5' end.

Lab

retro_mmus_150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_150 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032961	1 retrocopy	retro_btau_13,
Callithrix jacchus	ENSCJAG00000004610	1 retrocopy	retro_cjac_3333,
Echinops telfairi	ENSETEG00000000303	1 retrocopy	retro_etel_1526,
Homo sapiens	ENSG00000134049	1 retrocopy	retro_hsap_1156,
Gorilla gorilla	ENSGGOG00000027939	1 retrocopy	retro_ggor_903,
Mus musculus	ENSMUSG00000090000	1 retrocopy	retro_mmus_150 ,
Nomascus leucogenys	ENSNLEG00000011450	1 retrocopy	retro_nleu_2504,
Otolemur garnettii	ENSOGAG00000016626	1 retrocopy	retro_ogar_2152,
Pongo abelii	ENSPPYG00000009141	3 retrocopies	retro_pabe_2850, retro_pabe_2851, retro_pabe_962,
Pan troglodytes	ENSPTRG00000010002	1 retrocopy	retro_ptro_791,
Tupaia belangeri	ENSTBEG00000001443	4 retrocopies	retro_tbel_1530, retro_tbel_2783, retro_tbel_3343, retro_tbel_3429,
Tursiops truncatus	ENSTTRG00000001019	1 retrocopy	retro_ttru_1930,