RetrogeneDB ID: retro_mmus_2499

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:109373700..109374859(-)
• Located in intron of: ENSMUSG00000028552

Retrocopy information

• Ensembl ID: ENSMUSG00000083512
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Bzw1
• Ensembl ID: ENSMUSG00000051223
• Aliases: Bzw1, 1200015E15Rik, mKIAA0005
• Description: basic leucine zipper and W2 domains 1 [Source:MGI Symbol;Acc:MGI:1914132]

Sequence

>retro_mmus_2499
ATGAATAATCAAAAGCAGCAAAACCCAACGCTATCAGGCCAGCGTTTTAAAACCAGAAAAAGAGACGAAAAAGAGAGGTT
TGGCCCTACTCAGTTTCAAGACTGTATTATTCAAGGCTTCACTGAAACTGGCACTGATTTGGAAGCAGTAGCAAGTTTCT
TGACGCTTCTGGAGCAAAACTTGACTACCACCGCTTTGCAGAAACACTCTTTGACATCCTGGTGGCTGGCGGAATGCTGG
CCCCAGGTGGTACACTGGCAGATGACATGATGCGCACAGATGTCTGTGTGTGTGCAGCACAAGAAGACCTAGAGACCATG
CAAGCATTCACCCAGGCTTTTAACAAGCTAACCAGGCGCTACAGATACCCAGAGAAAGGTTTTGAAGATGAAGTTAAAAA
GTTACTGCTCTTCCTAAAGGGATTTTCAGAGCCGGAGAAGAACAAGCTCGCCATGTTGACTGGGGTCCTTCTGGCTAATG
GAACCCTTAATGCATCCATTCTTAACAGCCTTTATAATGAGAATTTGGTTAAAAAAAGGGTTTCAGCAGCTTTTGCTGTA
AAGCTCTTTAAATCATGGATAAATGAAAAGACATCAATGCAGTTGCTGCAAGTCTTCGGAGAGTCAGCATGGACAACAAA
CTGATGGAGCTGTTCCCTGCCAGTAAACAGAGTGATGGGCATTTCACTAAGTATTTCACTGAGGCGGGCTTGAAGGAGCT
TTCCGAGTATGTCCGCAACCAGCAGACCATTGGGGCTCGGAAGGAGCTCTGGAAGGAGCTGCAGGAGCAGATGTCCCACG
GGGACCCATTCAAGGACATAATTTTATATGTCAAGGAGGAGATGAAAAAAGTAACATTCCAGAACCAGTGGTGATTGGGA
TGGAGAGTCTGGTCCAGTGTGATGAGCACCGTGGAGTGGAACAAAAAAGAGGAGCTTGTAGCAGAACAAGCCATCAAGCA
CTTGAAGCAATGCAGCCCTCTCCTTGCTGCCTTCACTGCTAAAGGTCAGTCTGAGCTGACTCTGCTACTGGAGACCCAGG
AGTATTGCTATGACAACATTCACTTCATGAAAGCCTTCCAGAGAATAGTGGTGCTTTTTTATAAAGCTGAGGCCCTGAGT
GAAGAGCCCATTCTGAAGTGGTATAAAGACACACATGTT

Alignment

ORF - retro_mmus_2499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.95 %
• Parental protein coverage: 92.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNNQKQQKPTLSGQRFKTRKRDEKERFDPTQFQDCIIQGLTETGTDLEAVA-KFLDASGAKLDYRRYAET
          MNNQKQQ.PTLSGQRFKTRKRDEKERF.PTQFQDCIIQG.TETGTDLEAVA.KFLDASGAKLDY.R.AET
Retrocopy MNNQKQQNPTLSGQRFKTRKRDEKERFGPTQFQDCIIQGFTETGTDLEAVA<KFLDASGAKLDYHRFAET

Parental  LFDILVAGGMLAPGGTLADDMMRTDVCVFAAQEDLETMQAFAQVFNKLIRRYKYLEKGFEDEVKKLLLFL
          LFDILVAGGMLAPGGTLADDMMRTDVCV.AAQEDLETMQAF.Q.FNKL.RRY.Y.EKGFEDEVKKLLLFL
Retrocopy LFDILVAGGMLAPGGTLADDMMRTDVCVCAAQEDLETMQAFTQAFNKLTRRYRYPEKGFEDEVKKLLLFL

Parental  KGFSESERNKLAMLTGVLLANGTLNASILNSLYNENLVKEGVSAAFAVKLFKSWINEK-DINAVAASLRK
          KGFSE.E.NKLAMLTGVLLANGTLNASILNSLYNENLVK..VSAAFAVKLFKSWINEK.DINAVAASLR.
Retrocopy KGFSEPEKNKLAMLTGVLLANGTLNASILNSLYNENLVKKRVSAAFAVKLFKSWINEK<DINAVAASLRR

Parental  VSMDNRLMELFPANKQSVEHFTKYFTEAGLKELSEYVRNQQTIGARKELQKELQEQMSRGDPFKDIILYV
          VSMDN.LMELFPA.KQS..HFTKYFTEAGLKELSEYVRNQQTIGARKEL.KELQEQMS.GDPFKDIILYV
Retrocopy VSMDNKLMELFPASKQSDGHFTKYFTEAGLKELSEYVRNQQTIGARKELWKELQEQMSHGDPFKDIILYV

Parental  KEEMKKNNIPEPVVIGI-VWSSVMSTVEWNKKEELVAEQAIKHLKQYSPLLAAFTTQGQSELTLLLKIQE
          KEEMKK.........G..VWSSVMSTVEWNKKEELVAEQAIKHLKQ.SPLLAAFT..GQSELTLLL..QE
Retrocopy KEEMKKVTFQNQW*LGWRVWSSVMSTVEWNKKEELVAEQAIKHLKQCSPLLAAFTAKGQSELTLLLETQE

Parental  YCYDNIHFMKAFQKIVVLFYKAEVLSEEPILKWYKDAHV
          YCYDNIHFMKAFQ.IVVLFYKAE.LSEEPILKWYKD.HV
Retrocopy YCYDNIHFMKAFQRIVVLFYKAEALSEEPILKWYKDTHV

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	0.28 RPM	117.94 RPM
SRP007412_cerebellum	0.09 RPM	79.63 RPM
SRP007412_heart	0.00 RPM	50.00 RPM
SRP007412_kidney	0.10 RPM	108.74 RPM
SRP007412_liver	0.03 RPM	108.11 RPM
SRP007412_testis	0.05 RPM	158.85 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2499 was not detected

EST

No EST(s) were mapped for retro_mmus_2499 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_99083	641 libraries	401 libraries	29 libraries	1 library	0 libraries

The graphical summary, for retro_mmus_2499 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2499 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011878	1 retrocopy	retro_cfam_2150,
Choloepus hoffmanni	ENSCHOG00000003543	8 retrocopies	retro_chof_1519, retro_chof_2060, retro_chof_2092, retro_chof_2451, retro_chof_2517, retro_chof_689, retro_chof_726, retro_chof_838,
Cavia porcellus	ENSCPOG00000010449	1 retrocopy	retro_cpor_331,
Homo sapiens	ENSG00000082153	2 retrocopies	retro_hsap_2832, retro_hsap_2881,
Gorilla gorilla	ENSGGOG00000016296	1 retrocopy	retro_ggor_1997,
Mustela putorius furo	ENSMPUG00000012344	1 retrocopy	retro_mputfur_1174,
Mus musculus	ENSMUSG00000051223	3 retrocopies	retro_mmus_2499 , retro_mmus_751, retro_mmus_990,
Nomascus leucogenys	ENSNLEG00000006929	1 retrocopy	retro_nleu_621,
Pan troglodytes	ENSPTRG00000012791	1 retrocopy	retro_ptro_1949,