RetrogeneDB ID: retro_mmus_572

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:71704289..71705282(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Etv5
• Ensembl ID: ENSMUSG00000013089
• Aliases: Etv5, 1110005E01Rik, 8430401F14Rik, ERM
• Description: ets variant gene 5 [Source:MGI Symbol;Acc:MGI:1096867]

Sequence

>retro_mmus_572
TCACTTCCAGAACCTGGATCACAGCAACAAACATTTGCGGTCCCCCGGCCACCACATCAGCCCCTGCAAATGCCAAAGAT
GATGCCTGAAAGCCAGTATCCATCAGAACAGAGATTTCAGCGACAGCTGTCTGAGCCCAGCCATCCCTTCCCTCCTCAGT
CAGGAGTTCCTGGAGATAGTCGCCCCAGCTACCACCGGCAGATGTCAGAGCCCATTGTCCCCGCAGCTCCGCCACCCCTT
CAGGGATTCAAGCAGGAATACCATGACCCACTATATGAACATGGGGTCCCTGGGATGCCTGGTCCTCCAGCACATGGGTT
CCAGTCACCCATGGGGATCAAGCAGGAGCCCCGAGATTACTGTGCTGACTCAGAAGTGCCTAACTGCCAGTCATCCTACA
TGAGAGGCGGGTATTTCTCCAGCAGCCATGAAGGATTCCCGTATGAGAAGGACCCCAGGCTGTACTTTGATGATACTTGC
GTGGTACCCGAGAGACTGGAAGGCAAAGTCAAGCAGGAGCCCACCATGTATCGAGAGGGGCCTCCTTATCAGAGACGAGG
CTCTCTGCAGCTGTGGCAGTTCCTTGTCACCCTCCTGGATGACCCAGCCAATGCCCACTTCATCGCCTGGACTGACCCAG
GCATGGAATTTAAGCTCATAGAACCGGAAGAGGTTGCTCGCCGTTGGGGTATCCAGAAGAATCGGCCAGCCATGAACTAT
GGCAAGCTGAGCCGCTCTCTCCGCTATTACTATGAAAAGGGCATCATGCAGAAGGTGGCTGGGGAACGCTACATCTACAA
ATTTGTGTGTGACCCGGATGCACTCTTCTCTATGGCCTTCCCGGACAATCAGCGCCCGTTCCTGAAGGCAGAATCCGAAT
GCCCCCTCAATGAGGAGGACACGCTGCCTCTGACTCACTTTGAAGACAACCCTGCTTACCTCCTGGACAAGGATCGCTGC
AGCAGCCTCCCCTACGCCGAAGGCTTCGCTTAC

Alignment

ORF - retro_mmus_572 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.19 %
• Parental protein coverage: 64.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLPEPGSQQQTFAVPRPPHQPLQMPKMMPESQYPSEQRFQRQLSEPSHPFPPQSGVPGDSRPSYHRQMSE
          SLPEPGSQQQTFAVPRPPHQPLQMPKMMPESQYPSEQRFQRQLSEPSHPFPPQSGVPGDSRPSYHRQMSE
Retrocopy SLPEPGSQQQTFAVPRPPHQPLQMPKMMPESQYPSEQRFQRQLSEPSHPFPPQSGVPGDSRPSYHRQMSE

Parental  PIVPAAPPPLQGFKQEYHDPLYEHGVPGMPGPPAHGFQSPMGIKQEPRDYCADSEVPNCQSSYMRGGYFS
          PIVPAAPPPLQGFKQEYHDPLYEHGVPGMPGPPAHGFQSPMGIKQEPRDYCADSEVPNCQSSYMRGGYFS
Retrocopy PIVPAAPPPLQGFKQEYHDPLYEHGVPGMPGPPAHGFQSPMGIKQEPRDYCADSEVPNCQSSYMRGGYFS

Parental  SSHEGFPYEKDPRLYFDDTCVVPERLEGKVKQEPTMYREGPPYQRRGSLQLWQFLVTLLDDPANAHFIAW
          SSHEGFPYEKDPRLYFDDTCVVPERLEGKVKQEPTMYREGPPYQRRGSLQLWQFLVTLLDDPANAHFIAW
Retrocopy SSHEGFPYEKDPRLYFDDTCVVPERLEGKVKQEPTMYREGPPYQRRGSLQLWQFLVTLLDDPANAHFIAW

Parental  TGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPDALFSMAF
          T..GMEFKLIEPEEVARRWGIQKNRPAMNY.KLSRSLRYYYEKGIMQKVAGERY.YKFVCDPDALFSMAF
Retrocopy TDPGMEFKLIEPEEVARRWGIQKNRPAMNYGKLSRSLRYYYEKGIMQKVAGERYIYKFVCDPDALFSMAF

Parental  PDNQRPFLKAESECPLNEEDTLPLTHFEDNPAYLLDMDRCSSLPYTEGFAY
          PDNQRPFLKAESECPLNEEDTLPLTHFEDNPAYLLD.DRCSSLPY.EGFAY
Retrocopy PDNQRPFLKAESECPLNEEDTLPLTHFEDNPAYLLDKDRCSSLPYAEGFAY

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	0.14 RPM	65.93 RPM
SRP007412_cerebellum	0.35 RPM	41.77 RPM
SRP007412_heart	0.06 RPM	12.20 RPM
SRP007412_kidney	0.10 RPM	20.04 RPM
SRP007412_liver	0.03 RPM	4.81 RPM
SRP007412_testis	0.32 RPM	16.24 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_572 was not detected

EST

1 EST(s) were mapped to retro_mmus_572 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW230169	71704743	71704853	100	110	0	110

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_5067	1031 libraries	10 libraries	16 libraries	14 libraries	1 library

The graphical summary, for retro_mmus_572 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_572 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_572 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013420	1 retrocopy	retro_cfam_1414,
Mus musculus	ENSMUSG00000004151	1 retrocopy	retro_mmus_1056,
Mus musculus	ENSMUSG00000013089	1 retrocopy	retro_mmus_572 ,
Rattus norvegicus	ENSRNOG00000001785	2 retrocopies	retro_rnor_1500, retro_rnor_417,
Tarsius syrichta	ENSTSYG00000009845	1 retrocopy	retro_tsyr_2106,