RetrogeneDB ID: retro_mmus_1921

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:55292064..55292607(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082301
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ctsb
• Ensembl ID: ENSMUSG00000021939
• Aliases: Ctsb, CB
• Description: cathepsin B [Source:MGI Symbol;Acc:MGI:88561]

Sequence

>retro_mmus_1921
TCCTTGATCCATCTCTCTTGTCTGCTGGCACTCACCAGTGCCCATGACAAGCTTTCCTTCCACCCACTGTCGGATGACCT
GATTAACTACATCAACAGGCAGATTATAACATGGCAGGCTGAACGCAACTTCTACAATGTTGACATAAGCTATCTGAAGA
AGCTGTGTGGTACCATCCTGGGTGGACCCAAGGTGCCAGAAAGGGTTGGGTTCAGTGATGACATCAATCTACCTGAAACT
TTTGATACAAAGAAACAGTGGTCCAACTGCTCCATCATCGAACAGATTAGAAACCAGGGGTCCTGCGGCTCTTGTTGGGA
ATTTGGGGCAGTGGAAGCCATTTCTGACCAAATCTGCCTTCACACCAATGGCCAAGCCAACAATGGAGGTGTCTGCCGAG
GACCTGCTTACTCGTTGTGGCATCCAGTGTAGGGACGGCTGTAATGGTGGCTATCCCTCTGGAGCATGGGCTTTTGGATG
ATAAAAGGCCTGGTTTCTGGCAGAGTCTACATTTCTCATGAAGGTTGCTTAATGGTAAGCATA

Alignment

ORF - retro_mmus_1921 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.14 %
• Parental protein coverage: 53.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLILLSCLLALTSAHDKPSFHPLSDDLINYINKQNTTWQAGRNFYNVDISYLKKLCGTVLGGPKLPGRVA
          SLI.LSCLLALTSAHDK.SFHPLSDDLINYIN.Q..TWQA.RNFYNVDISYLKKLCGT.LGGPK.P.RV.
Retrocopy SLIHLSCLLALTSAHDKLSFHPLSDDLINYINRQIITWQAERNFYNVDISYLKKLCGTILGGPKVPERVG

Parental  FGEDIDLPETFDAREQWSNCPTIGQIRDQGSCGSCWAFGAVEAISDRTCIHTNGRVN-VEVSAEDLLTCC
          F..DI.LPETFD...QWSNC..I.QIR.QGSCGSCW.FGAVEAISD..C.HTNG..N..EVSAEDLLT.C
Retrocopy FSDDINLPETFDTKKQWSNCSIIEQIRNQGSCGSCWEFGAVEAISDQICLHTNGQAN>MEVSAEDLLTRC

Parental  GIQCGDGCNGGYPSGAWS-FWTKKGLVSGGVYNSHVGCLPYTI
          GIQC.DGCNGGYPSGAW..FW..KGLVSG.VY.SH.GCL...I
Retrocopy GIQCRDGCNGGYPSGAWA<FWMIKGLVSGRVYISHEGCLMVSI

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	0.00 RPM	440.16 RPM
SRP007412_cerebellum	0.04 RPM	448.28 RPM
SRP007412_heart	0.03 RPM	394.14 RPM
SRP007412_kidney	0.02 RPM	603.19 RPM
SRP007412_liver	0.00 RPM	584.21 RPM
SRP007412_testis	0.05 RPM	43.54 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1921 was not detected

EST

No EST(s) were mapped for retro_mmus_1921 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_87614	621 libraries	230 libraries	154 libraries	60 libraries	7 libraries

The graphical summary, for retro_mmus_1921 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_1921 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1921 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164733	1 retrocopy	retro_hsap_3032,
Loxodonta africana	ENSLAFG00000007380	1 retrocopy	retro_lafr_1150,
Monodelphis domestica	ENSMODG00000012029	6 retrocopies	retro_mdom_1066, retro_mdom_1067, retro_mdom_1199, retro_mdom_1707, retro_mdom_1973, retro_mdom_1985,
Mus musculus	ENSMUSG00000021939	1 retrocopy	retro_mmus_1921 ,
Mus musculus	ENSMUSG00000032359	1 retrocopy	retro_mmus_3643,