RetrogeneDB ID: retro_mmus_793

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:58508793..58509261(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000085342
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl24
• Ensembl ID: ENSMUSG00000022601
• Aliases: Zbtb11, 9230110G02Rik, ZNF-U69274
• Description: ribosomal protein L24 [Source:MGI Symbol;Acc:MGI:1915443]

Sequence

>retro_mmus_793
AGGGTCGAGCTGTGCAGTTTCAGCGGGTACAAGATCTACCCGGGACACGGGCGGCGCTACACCAGGACCGACGGGAAGGT
TTTCCAGTTTCTTAATGCAAAATGTGAGTCAGCATTCCTTTCCAAAAGGAATCCTCGGCAGATAAACTGGACTGTCCTCA
ACAGAAGGAAACACAAGAAAGGGCAGTCGGAAGAAATTCAAAAGAAAAGAACCCGCCGTGCAGTCAAATTCCAACGAGCC
ATCACTGGTGCATCTCTTGCTGATATAATGGCCAAGAGGAATCAGAAACCAGAGGTTAGGAAAGCCCAGCGAGAGCAGGC
TATCAGGGCTGCCAAGGAAGCAAAAAAGGCTAAGCAGGCATCAAAGAAGACAGCAATGGCTGCTGCCAAGGCCCCCACAA
AGGCAGCACCTAAACAAAAGATTGTGAAGTCTGTGAAGATTTCTGCCCCCAGAGTTGGTGGGAAACGC

Alignment

ORF - retro_mmus_793 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.79 %
• Parental protein coverage: 99.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKKR
          .VELCSFSGYKIYPGHGRRY.RTDGKVFQFLNAKCESAFLSKRNPRQINWTVL.RRKHKKGQSEEIQKKR
Retrocopy RVELCSFSGYKIYPGHGRRYTRTDGKVFQFLNAKCESAFLSKRNPRQINWTVLNRRKHKKGQSEEIQKKR

Parental  TRRAVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKTAMAAAKAPTKAAPKQK
          TRRAVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKTAMAAAKAPTKAAPKQK
Retrocopy TRRAVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKTAMAAAKAPTKAAPKQK

Parental  IVKPVKVSAPRVGGKR
          IVK.VK.SAPRVGGKR
Retrocopy IVKSVKISAPRVGGKR

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	0.21 RPM	83.94 RPM
SRP007412_cerebellum	0.00 RPM	81.85 RPM
SRP007412_heart	0.47 RPM	59.33 RPM
SRP007412_kidney	0.17 RPM	59.77 RPM
SRP007412_liver	0.16 RPM	60.76 RPM
SRP007412_testis	0.09 RPM	67.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_793 was not detected

EST

No EST(s) were mapped for retro_mmus_793 retrocopy.

TSS

No TSS is located nearby retro_mmus_793 retrocopy 5' end.

Lab

retro_mmus_793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_793 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022601	13 retrocopies	retro_mmus_1398, retro_mmus_1418, retro_mmus_1555, retro_mmus_2145, retro_mmus_2429, retro_mmus_2434, retro_mmus_2870, retro_mmus_2981, retro_mmus_3208, retro_mmus_3384, retro_mmus_500, retro_mmus_793 , retro_mmus_87,