RetrogeneDB ID: retro_mmus_3576

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:13377868..13378678(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080818
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Med4
• Ensembl ID: ENSMUSG00000022109
• Aliases: Med4, 2410046H15Rik, DRIP36, HSPC126, TRAP36, Vdirp, Vdrip
• Description: mediator of RNA polymerase II transcription, subunit 4 homolog (yeast) [Source:MGI Symbol;Acc:MGI:1914631]

Sequence

>retro_mmus_3576
ATGGTGACTTCTTCAAGTGGTGAGAAGGAAAAAGAGCGGATGGGAGGCGTTTCGGGAATGGCCAGCCTTGGCAGTACATG
AGAGCGGCTTCTATCTGTGCTGGAAGATCTGGGGGTCTTCTCCAGGGAACTTATAGAAATGCTTGCAATTTCAAGAAATC
AGAAGCTGTTACAGCTGGAAGAGGAAAACCAGGTCTTGGAGTTGCTAATTCACCGAGATGGGGACTTCCAAGAACTAATG
AAATTAGCACTTAATCAGGGAAAAGTCCACCATGAAATGCAGGCTTTAGAGAAAGAAGTAGAGAAGAGAGACAGTGATAT
TCAGCAGCTTCAGAAACAGCTGAAAGAGGCAGAGCAAATCCTGGCAACAGCTGTTTACCAGGCAAAGGAGAAACTCAAGT
CAATAGAGAAAGCAAGAAAAGGTGCTATCTCCTCTGAAGAAATCATTAAATATGCACACAGGATTAGTGCAAGTAATGCT
GTCTGTGCTCCACTGACTTGGGTTCCAGGAGACCCTCGGAGGCCATACCCAACAGATTTAGAGATGAGAAGTGGATTGTT
GGGTCAGATGAACAATCCTTCCACCAGTGGTGTGAATGGTCACCTCCCGGGCGATGCCCTTGCAGCAGTTAGACTGCCAG
ATGTCCTTGCTCCACAGTACCCATGGCAGTCAAATGACATGTCTGTGAACATGCTACCACCAAATCACAGCAGTGACTTT
CTGTTGGAGCCTCCTGGGCACAACAAAGAAAATGAAGATGATGTTGAGGTTATGTCAATAGATTCTTCGAGCAGCAGTAG
CGATTCTGAC

Alignment

ORF - retro_mmus_3576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASSSGEKEKERMGGVSGMAGLGSTRERLLSALEDLEVLSRELIEMLAISRNQKLLQLEEENQVLELLI
          M..SSSGEKEKERMGGVSGMA.LGST.ERLLS.LEDL.V.SRELIEMLAISRNQKLLQLEEENQVLELLI
Retrocopy MVTSSSGEKEKERMGGVSGMASLGST*ERLLSVLEDLGVFSRELIEMLAISRNQKLLQLEEENQVLELLI

Parental  HRDGDFQELMKLALNQGKVHHEMQALEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARK
          HRDGDFQELMKLALNQGKVHHEMQALEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARK
Retrocopy HRDGDFQELMKLALNQGKVHHEMQALEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARK

Parental  GAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTSGVNGHLPGDALAAG
          GAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTSGVNGHLPGDALAA.
Retrocopy GAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTSGVNGHLPGDALAAV

Parental  RLPDVLAPQYPWQSNDMSVNMLPPNHSSDFLLEPPGHNKENEDDVEVMSTDSSSSSSDSD
          RLPDVLAPQYPWQSNDMSVNMLPPNHSSDFLLEPPGHNKENEDDVEVMS.DSSSSSSDSD
Retrocopy RLPDVLAPQYPWQSNDMSVNMLPPNHSSDFLLEPPGHNKENEDDVEVMSIDSSSSSSDSD

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	13.85 RPM
SRP007412_cerebellum	0.00 RPM	16.41 RPM
SRP007412_heart	0.03 RPM	13.07 RPM
SRP007412_kidney	0.00 RPM	11.32 RPM
SRP007412_liver	0.03 RPM	7.95 RPM
SRP007412_testis	0.00 RPM	20.31 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3576 was not detected

EST

No EST(s) were mapped for retro_mmus_3576 retrocopy.

TSS

No TSS is located nearby retro_mmus_3576 retrocopy 5' end.

Lab

retro_mmus_3576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3576 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003718	1 retrocopy	retro_amel_1882,
Canis familiaris	ENSCAFG00000004451	1 retrocopy	retro_cfam_1792,
Callithrix jacchus	ENSCJAG00000009256	1 retrocopy	retro_cjac_3937,
Dasypus novemcinctus	ENSDNOG00000018064	1 retrocopy	retro_dnov_1342,
Myotis lucifugus	ENSMLUG00000009265	1 retrocopy	retro_mluc_178,
Mustela putorius furo	ENSMPUG00000001437	1 retrocopy	retro_mputfur_162,
Mus musculus	ENSMUSG00000022109	1 retrocopy	retro_mmus_3576 ,
Sorex araneus	ENSSARG00000001473	1 retrocopy	retro_sara_353,
Tupaia belangeri	ENSTBEG00000014259	1 retrocopy	retro_tbel_292,