RetrogeneDB ID: retro_mmus_720

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:70358137..70358784(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082145
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fgfr1op2
• Ensembl ID: ENSMUSG00000040242
• Aliases: Fgfr1op2, 1500031J01Rik
• Description: FGFR1 oncogene partner 2 [Source:MGI Symbol;Acc:MGI:1914779]

Sequence

>retro_mmus_720
ATGAGCTGCACCATTGAGAAAGCACTTGCTGTCGCTAAAGCCCTTGTTGAAAGATTGAGAGATCATGATGATGCAGCGGA
GTCTCTCATCGAGCAGACCACTGCCCTCAGCAAGCGAGTGGAAGCGATGAAGCAGTATCAGGAAGAAATCCAAGAACTTA
ATGAAGTAGCAAGATATCAGCCACGATCCACACTAGTTATGGGAATCCAACAAGAAAACAGACAAATCAGAGAATTAACA
ACAAGAGAACAAAGAACTGCGGACATCCCTGGAAGAGCACCAGTCTGCCCTGGAACTGATAATGAGCAAGTACCGAGAGC
AGATGTTCAGACTGCTCATGGCCAGCAAGAAAGATGACCCAGGTATAATAATGAAGTTAATAGAGCAGCACTCAAAGGAG
TTGCAAGCACATGTTGACCAAATCACCGAGATGGCAGCAGTAATGAGAAAAGATATTGAAATTGACGAGCAACAGGGTTG
CAAGGAACAGGAGCGGGATATTTCAACTTGAACAAGAAAATAAAGGCTTGAGAGAGACCCTTCAGATAACTTGAGAATCC
TTTTTAAACCTTCGGAAGGATGATGCGTCAGAGAGTACATCTCTGTCCCCCTTAGTGACTAACAGTGACCTGAGTCTGAG
GAAGAGC

Alignment

ORF - retro_mmus_720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSCTIEKALADAKALVERLRDHDDAAESLIEQTTALSKRVEAMKQYQEEIQELNEVARHRPRSTLVMGIQ
          MSCTIEKALA.AKALVERLRDHDDAAESLIEQTTALSKRVEAMKQYQEEIQELNEVAR..PRSTLVMGIQ
Retrocopy MSCTIEKALAVAKALVERLRDHDDAAESLIEQTTALSKRVEAMKQYQEEIQELNEVARYQPRSTLVMGIQ

Parental  QENRQIREL-QQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKLKEQHSKELQAHVD
          QENRQIREL.QQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKL.EQHSKELQAHVD
Retrocopy QENRQIREL>QQENKELRTSLEEHQSALELIMSKYREQMFRLLMASKKDDPGIIMKLIEQHSKELQAHVD

Parental  QITEMAAVMRKAIEIDEQQGCKEQER-IFQLEQENKGLREILQITRESFLNLRKDDASESTSLSALVTNS
          QITEMAAVMRK.IEIDEQQGCKEQER.IFQLEQENKGLRE.LQIT.ESFLNLRKDDASESTSLS.LVTNS
Retrocopy QITEMAAVMRKDIEIDEQQGCKEQER>IFQLEQENKGLRETLQIT*ESFLNLRKDDASESTSLSPLVTNS

Parental  DLSLRKS
          DLSLRKS
Retrocopy DLSLRKS

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	0.37 RPM	77.24 RPM
SRP007412_cerebellum	0.78 RPM	41.34 RPM
SRP007412_heart	0.03 RPM	55.88 RPM
SRP007412_kidney	0.69 RPM	49.72 RPM
SRP007412_liver	0.38 RPM	40.83 RPM
SRP007412_testis	5.17 RPM	130.90 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_720 was not detected

EST

No EST(s) were mapped for retro_mmus_720 retrocopy.

TSS

No TSS is located nearby retro_mmus_720 retrocopy 5' end.

Lab

retro_mmus_720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_720 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006966	2 retrocopies	retro_dnov_2342, retro_dnov_2594,
Equus caballus	ENSECAG00000016890	1 retrocopy	retro_ecab_988,
Homo sapiens	ENSG00000111790	1 retrocopy	retro_hsap_994,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486,
Monodelphis domestica	ENSMODG00000016618	2 retrocopies	retro_mdom_1788, retro_mdom_244,
Mus musculus	ENSMUSG00000040242	2 retrocopies	retro_mmus_3669, retro_mmus_720 ,
Pongo abelii	ENSPPYG00000004375	1 retrocopy	retro_pabe_839,
Pan troglodytes	ENSPTRG00000004783	1 retrocopy	retro_ptro_756,
Tupaia belangeri	ENSTBEG00000011581	2 retrocopies	retro_tbel_3732, retro_tbel_4608,