RetrogeneDB ID: retro_mmus_2983

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:141406636..141407191(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000091083
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rangrf
• Ensembl ID: ENSMUSG00000032892
• Aliases: Rangrf, 2400006H24Rik, Mog1, Rangnrf
• Description: RAN guanine nucleotide release factor [Source:MGI Symbol;Acc:MGI:1889073]

Sequence

>retro_mmus_2983
ATGGAGCCCACCAGAAACTGTCCACTGTTCGGAGGCGCCTTCTCCGCCATCCTCCCTACAGGGGCCATTGATGTGAGTGA
CCTCCGACCGGTGCCAGACAACCAAGAAGTTTTCTGCCATCCTGTGACCAACCAGAGTCTGATCATAGAACTTCTGGAGC
TGCAGGCCCACGTGCAGGGCGAAGCGGCTGCGCGGTACCATTTTGAGGACGTTGGCCGGGTGCAGGGGGCTAGGGCTGTG
CACGTGCTATCTGTACAGCCTCTCTGTTTGGAGAACTTATCCCTGAGAGGCTGCTGTCAGGATGCCTGGTCCCTTTCTGG
CAAGCAGCAGGTAGCTAAAGAAAACCAGCAGGTAGCAAAGGATGTCACACTGCATCAGGCCTTGCTGCGGCTGCCCCGGT
ATCAGACTGATCTTTTGCTCACCTTCAATCAGCCCCCGTGTCACAGCAGGTCTCTTGGCCCTGAAAATCTGTCATGTCCA
CCTTGGAGCCTGAGTAACTTTGAACAGCCGCTAACTAGTTTGACTCTTCATGATCCCAACCTCTTTGGTCCCCAG

Alignment

ORF - retro_mmus_2983 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPNRNCPLFGGAFSAILPTGAIDVSDLRPVPDNQEVFCHPVTDQSLIIELLELQAHVQGEAAARYHFED
          MEP.RNCPLFGGAFSAILPTGAIDVSDLRPVPDNQEVFCHPVT.QSLIIELLELQAHVQGEAAARYHFED
Retrocopy MEPTRNCPLFGGAFSAILPTGAIDVSDLRPVPDNQEVFCHPVTNQSLIIELLELQAHVQGEAAARYHFED

Parental  VGRVQGARAVHVLSVQPLCLENLSLRGCCQDAWSLSGKQQVAKENQQVAKDVTLHQALLRLPQYQTDLLL
          VGRVQGARAVHVLSVQPLCLENLSLRGCCQDAWSLSGKQQVAKENQQVAKDVTLHQALLRLP.YQTDLLL
Retrocopy VGRVQGARAVHVLSVQPLCLENLSLRGCCQDAWSLSGKQQVAKENQQVAKDVTLHQALLRLPRYQTDLLL

Parental  TFNQPPCHSRSLGPENLSCPPWSLSNFEQLVTSLTLHDPNLFGPQ
          TFNQPPCHSRSLGPENLSCPPWSLSNFEQ..TSLTLHDPNLFGPQ
Retrocopy TFNQPPCHSRSLGPENLSCPPWSLSNFEQPLTSLTLHDPNLFGPQ

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	0.09 RPM	0.12 RPM
SRP007412_cerebellum	0.04 RPM	0.22 RPM
SRP007412_heart	0.03 RPM	0.09 RPM
SRP007412_kidney	0.02 RPM	0.10 RPM
SRP007412_liver	0.03 RPM	0.00 RPM
SRP007412_testis	0.27 RPM	0.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2983 was not detected

EST

No EST(s) were mapped for retro_mmus_2983 retrocopy.

TSS

No TSS is located nearby retro_mmus_2983 retrocopy 5' end.

Lab

retro_mmus_2983 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2983 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012555	1 retrocopy	retro_chof_14,
Dasypus novemcinctus	ENSDNOG00000018164	1 retrocopy	retro_dnov_2261,
Dipodomys ordii	ENSDORG00000007147	2 retrocopies	retro_dord_325, retro_dord_346,
Macropus eugenii	ENSMEUG00000006399	2 retrocopies	retro_meug_1091, retro_meug_220,
Mus musculus	ENSMUSG00000032892	2 retrocopies	retro_mmus_175, retro_mmus_2983 ,
Rattus norvegicus	ENSRNOG00000004980	4 retrocopies	retro_rnor_1148, retro_rnor_2982, retro_rnor_2983, retro_rnor_759,