RetrogeneDB ID: retro_mmus_199

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:163087105..163087561(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000070708
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BC048502
• Ensembl ID: ENSMUSG00000053508
• Aliases: None
• Description: cDNA sequence BC048502 [Source:MGI Symbol;Acc:MGI:2652828]

Sequence

>retro_mmus_199
ATGGAGCCAGAATCCATAGAAATTTGTCCTTATAACCCTCACCACCGAATCCCGCTCAGCAGGTTCCAGTACCACCTGGC
GTCATGCAGGAAGAAGAACCCCAAGAAAGCCAAAAAGATGGCCAGCTGTAAATACAACGCCTGCCACGTGGTTCCCATCA
GAAAGCTGGCTGAACATGAAGCTACCTGTGTCAACAGGAGCTCCGTGGAGGAAGAGGACACATTAGGCCCTCTGCAAGTC
AGCCTCCCACAGCCGCAGAACCAGGACACACTACAGGTTCGTTGGCTTTCCAACCCTGACATTTGGAATGTTGACGGCGC
CAACTGTCACCCAATGTTCGTCCTTAAGAGTTTTGTTCCCCAAAAACTTGTTTGTGAAAGTGACATCCAAGAGTCACGGG
GAGGAGACCAATGCCCAGAAGATCCTCAGACTAGGACCAGGAAGGCAAACTTCTAG

Alignment

ORF - retro_mmus_199 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELESIELCPYDPNHRIPASRLQYHLASCKKKNPKIAKKMANCKYNACHVVPIKRLKEHEANCINRTAVD
          ME.ESIE.CPY.P.HRIP.SR.QYHLASC.KKNPK.AKKMA.CKYNACHVVPI..L.EHEA.C.NR..V.
Retrocopy MEPESIEICPYNPHHRIPLSRFQYHLASCRKKNPKKAKKMASCKYNACHVVPIRKLAEHEATCVNRSSVE

Parental  DE-PLNLQKITHPVFEENENFSSAGSQFPDPDVWNVDHAHHFPSFVLETFAPKKLVCESDSRD
          .E..L.......P...............PD...WNVD.A...P.FVL..F.P.KLVCESD...
Retrocopy EEDTLGPLQVSLPQPQNQDTLQVRWLSNPD--IWNVDGANCHPMFVLKSFVPQKLVCESDIQE

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	0.07 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.17 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	113.52 RPM	48.21 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_199 was not detected

EST

No EST(s) were mapped for retro_mmus_199 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_82730	1057 libraries	11 libraries	1 library	1 library	2 libraries
TSS #2	TSS_82731	1057 libraries	9 libraries	2 libraries	1 library	3 libraries
TSS #3	TSS_82732	1058 libraries	7 libraries	1 library	0 libraries	6 libraries

The graphical summary, for retro_mmus_199 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_199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_199 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1938

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029590	1 retrocopy	retro_acar_141,
Ailuropoda melanoleuca	ENSAMEG00000000958	1 retrocopy	retro_amel_91,
Cavia porcellus	ENSCPOG00000023851	1 retrocopy	retro_cpor_93,
Felis catus	ENSFCAG00000031316	1 retrocopy	retro_fcat_1,
Mustela putorius furo	ENSMPUG00000005664	1 retrocopy	retro_mputfur_116,
Mus musculus	ENSMUSG00000053508	1 retrocopy	retro_mmus_199 ,
Rattus norvegicus	ENSRNOG00000036830	1 retrocopy	retro_rnor_1938,