RetrogeneDB ID: retro_mmus_1722

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:50134794..50135508(+)
• Located in intron of: ENSMUSG00000024507

Retrocopy information

• Ensembl ID: ENSMUSG00000085939
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cd63
• Ensembl ID: ENSMUSG00000025351
• Aliases: Cd63, C75951, ME491, Tspan30
• Description: CD63 antigen [Source:MGI Symbol;Acc:MGI:99529]

Sequence

>retro_mmus_1722
ATGGCGGTGGAAGGAGGAATGAAGTGTGTCAAGTTTTTGCTCTACGTTCTCCTGCTGGCCTTCTGCACCTGTGCAGTGGG
ATTGATCGCCATTGGTGTAGCGGTTCAGGTTGTCTTGAAGCAGGCTATTACCTATGAGACTACTGCTGGCTCGCTGTTGC
CTGTGGTCATCATTGCAGTGGGTGCCTTCCTCTTCCTGGTGGCCTTTGTGGGCTGCTGTGGCGCCTGCAAGGAGAACTAC
TGTCTCATGATTACATTTGCCATCTTCCTGTCTCTTATCATGCTTGTGGAGGTGGCTGTGGCCATTGCTGGCTATGTGTT
TAGAGACCAGGTGAAGTCAGAGTTTAATAAAAGCTTCCAGCAGCAGATGCAGAATTACCTTAAAGACAACAAAACAGCCA
CTATTTTGGACAAATTGCAGAAAGAAAATAACTGCTGTGGAGCTTCTAACTACACAGACTGGGAAAACATCCCCGTCATG
GCCAAGGACAGAGTCCCCGATTCTTGCTGCATCAACATAACTGTGGGCTGTGGGAATGATTTCAAGGAATCCACTATCCA
TACCCAGGGCTGCGTGGAGACTATAGCAATATGGCTAAGGAAGAACATACTGCTGGTGGCTGCAGTGGCCCTGGGCATTG
CTTTTGTGGAGGTCTTGGGAATTATCTTCTCCTGCTGTCTGGTGAAAAGTATTCGAAGTGGCCATGAAGTAATG

Alignment

ORF - retro_mmus_1722 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVEGGMKCVKFLLYVLLLAFCACAVGLIAIGVAVQVVLKQAITHETTAGSLLPVVIIAVGAFLFLVAFV
          MAVEGGMKCVKFLLYVLLLAFC.CAVGLIAIGVAVQVVLKQAIT.ETTAGSLLPVVIIAVGAFLFLVAFV
Retrocopy MAVEGGMKCVKFLLYVLLLAFCTCAVGLIAIGVAVQVVLKQAITYETTAGSLLPVVIIAVGAFLFLVAFV

Parental  GCCGACKENYCLMITFAIFLSLIMLVEVAVAIAGYVFRDQVKSEFNKSFQQQMQNYLKDNKTATILDKLQ
          GCCGACKENYCLMITFAIFLSLIMLVEVAVAIAGYVFRDQVKSEFNKSFQQQMQNYLKDNKTATILDKLQ
Retrocopy GCCGACKENYCLMITFAIFLSLIMLVEVAVAIAGYVFRDQVKSEFNKSFQQQMQNYLKDNKTATILDKLQ

Parental  KENNCCGASNYTDWENIPGMAKDRVPDSCCINITVGCGNDFKESTIHTQGCVETIAIWLRKNILLVAAAA
          KENNCCGASNYTDWENIP.MAKDRVPDSCCINITVGCGNDFKESTIHTQGCVETIAIWLRKNILLVAA.A
Retrocopy KENNCCGASNYTDWENIPVMAKDRVPDSCCINITVGCGNDFKESTIHTQGCVETIAIWLRKNILLVAAVA

Parental  LGIAFVEVLGIIFSCCLVKSIRSGYEVM
          LGIAFVEVLGIIFSCCLVKSIRSG.EVM
Retrocopy LGIAFVEVLGIIFSCCLVKSIRSGHEVM

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	0.19 RPM	24.86 RPM
SRP007412_cerebellum	0.04 RPM	31.78 RPM
SRP007412_heart	0.50 RPM	80.41 RPM
SRP007412_kidney	3.70 RPM	479.91 RPM
SRP007412_liver	0.00 RPM	4.64 RPM
SRP007412_testis	0.05 RPM	10.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1722 was not detected

EST

No EST(s) were mapped for retro_mmus_1722 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_59717	85 libraries	26 libraries	116 libraries	126 libraries	719 libraries
TSS #2	TSS_59718	524 libraries	358 libraries	183 libraries	6 libraries	1 library
TSS #3	TSS_59719	401 libraries	309 libraries	302 libraries	56 libraries	4 libraries

The graphical summary, for retro_mmus_1722 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_1722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1722 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011931	1 retrocopy	retro_btau_234,
Callithrix jacchus	ENSCJAG00000007935	1 retrocopy	retro_cjac_4051,
Cavia porcellus	ENSCPOG00000009142	1 retrocopy	retro_cpor_676,
Mus musculus	ENSMUSG00000025351	1 retrocopy	retro_mmus_1722 ,
Mus musculus	ENSMUSG00000058254	1 retrocopy	retro_mmus_157,