RetrogeneDB ID: retro_mmus_3557

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:162566847..162567240(+)
• Located in intron of: ENSMUSG00000040855

Retrocopy information

• Ensembl ID: ENSMUSG00000059461
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Kxd1
• Ensembl ID: ENSMUSG00000055553
• Aliases: Kxd1, 0610030B01Rik, 2810422J05Rik, C78305
• Description: KxDL motif containing 1 [Source:MGI Symbol;Acc:MGI:1922870]

Sequence

>retro_mmus_3557
GACGCCAACATGCAGATCTTCGTGAAGACCCTGCCGGGCAAGACCATCACTCTTGAGGTCGAGCCCAGTGACACCATCGA
GAATGTCAAGGCCAAGATCCAAGACAAGGAAGGCATCCCACCTGACCAGCAGAGGCTGATATTCGCGGGCAAACAGCTGG
AGGATGGCCGCACCCTGTCCGACTACAACATCCAGAAAGAGTCCACCTTGCACCTGGTGCTGCGTCTGCGCGGTGGCATC
ATTGAGCCATCCCTTCGTCAGCTTGCCCAGAAGTACAACTGTGACAAGATGATCTGCCGCAAGTGCTACGCACGCCTGCA
CCCTCGTGCAGTCAACTGCCGCAAGAAGAAGTGCGGCCATACCAACAACCTGTGCCCCAAGAAGAAGGTCAAA

Alignment

ORF - retro_mmus_3557 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.47 %
• Parental protein coverage: 56.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DANMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL
          DANMQIFVKTL.GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL
Retrocopy DANMQIFVKTLPGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTL

Parental  HLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKVK
          HLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNL.PKKKVK
Retrocopy HLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLCPKKKVK

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	18.08 RPM
SRP007412_cerebellum	0.00 RPM	16.80 RPM
SRP007412_heart	0.16 RPM	47.38 RPM
SRP007412_kidney	0.02 RPM	40.44 RPM
SRP007412_liver	0.05 RPM	28.18 RPM
SRP007412_testis	0.00 RPM	25.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3557 was not detected

EST

No EST(s) were mapped for retro_mmus_3557 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_156207	7 libraries	2 libraries	56 libraries	117 libraries	890 libraries

The graphical summary, for retro_mmus_3557 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_3557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3557 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010545	1 retrocopy	retro_btau_689,
Echinops telfairi	ENSETEG00000003390	2 retrocopies	retro_etel_1213, retro_etel_2129,
Macropus eugenii	ENSMEUG00000013150	1 retrocopy	retro_meug_2148,
Monodelphis domestica	ENSMODG00000003489	1 retrocopy	retro_mdom_1623,
Mus musculus	ENSMUSG00000055553	6 retrocopies	retro_mmus_1117, retro_mmus_3557 , retro_mmus_799, retro_mmus_800, retro_mmus_802, retro_mmus_804,
Rattus norvegicus	ENSRNOG00000019971	2 retrocopies	retro_rnor_2808, retro_rnor_812,