RetrogeneDB ID: retro_mmus_207

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:50608636..50610709(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000092012
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Crnkl1
• Ensembl ID: ENSMUSG00000001767
• Aliases: Crnkl1, 1200013P10Rik, 5730590A01Rik, C80326, crn
• Description: Crn, crooked neck-like 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:1914127]

Sequence

>retro_mmus_207
ATGGCGTCATCCACCGTGGCCAAGAAAGAGCAGCGCCTTCCTAAAGTGGCCCAGGTCAAAAACAAAGCTGCGGCCGAGGT
GCAGATAACTGCAGAGCAGCTCTTAAGGGAAGCTAAAGAGAGAGAACTCGAGCTCCTCGCGCCTCCACCTCAGCAGAAGA
TCACAGACGCAGAAGAATTCAATGATTACAAACTCCGGAGAAGAAAGGCCTTTGAAGAAAACCTCAGACAGAAGAGGACT
GTGATTAGCAACTGGATCAAATACGCACAATGGGAGGAAAGCCTGAAGGAGCTCGATAGGGCTCGATCCATATACGAGCG
TGCTTTAGATGTGGACTACCGCAATCTTACCCTCTGGCTGAAATACGCAGAGATGGAGATGAAGAACCGCCAGGTCAACC
ATGCCCGAAACATCTGGGACCGTGCCATCACAACTCTGCCCCGAGTCAAGCAGTTGTGGTACAAGTACACGTACATGGAG
GAGCTGTTGGGCAACGTCGCTGGTGCTCGTCAGGTGTTTGAGCGCTGGATGGAATGGCAGCCTGAGGAGCAGGCCTGGCA
CTCGTACATCAACTTGGAGCTGAGGTACAAAGAGGTGGAGCGGGCCCGCACCATTTATGAACGCTTTGTGCTCGTGCACC
CTGCTGTGAAGAACTGGATCAAGTATGCTCGGTTTGAAGAGCGGCACGCTTCTGTTGCTCATGCGCGGAAAGTCTACGAG
AGGGCCGTGGAGTTTTTCGGGGAGGAGCATATGGACCAACACCTCTATGTGGCCTTTGCAAAATTCGAGGAGAATCAGAA
AGAACTGGAAAGGGTGCGAGTTATCTACAGATATGCCCTGGATAGGATTTCCAAACAGGAGGCCCAAGAACTCTTGACAA
ACTACACCATCTTTGAGAAGAAGTTTGGTGAGCGGAGGGATGTAGAAGAGAGCATCGTGAGAAAACGCCGATTCCACTAC
GAAGAAGAAGTGAAGGCTAATCCGCACAATTACGACGCGTGGTTTGATTACTTACGCTTGGTGGAAAGTGAGGCAGAAGC
CGACACCGTGCGGGAAGTCTATGAGAGAGCCATCGCCAGTGTGCCACCGGTGCTGGAGAAGAGGCACTGGAAGCGCTACA
TCTACCTCTGGGTTAACTATGCGCTCTATGAAGAGCTGGAGGCCAAGGATCCCGAGAGGACGAGACGCGTCTATCAAGCG
TCTCTGCAGCTCATTCCTCACACAAAGTTCACCTTTGCCAAAATGTGGTTGTATTATGCCCAGTTTGAAATACGGCAGAA
GAATCTGCCATTGGCCAGAAGAGCTTTGGGCACTTCCCTAGGCAAATGTCCAAAGAACAAGTTGTTCAAAGGCTACATAG
CCCTGGAGCTGCAGCTTCGAGAGTTTGACAGATGCAGGAAGCTTTATGAGAAGTTTCTGGAATTCGGACCTGAAAATTGT
ACCTCGTGGATAAAGTTTGCAGAGTTAGAGACAATCCTTGGTGATGTTGAGAGAGCTCGGGCAATCTATGAGTTAGCCAT
CAGCCAGCCGCGCTTGGATATGCCAGAGCTACTTTGGAAATCCTATATTGATTTTGAGATGGAGCAGGAAGAGCCTGAGA
GAACACGGAACCTTTACCGACGGTTGCTTCAGAGAACACAGCACGTCAAGGTGTGGATCAGTTTGGCTCAGTTTGAGTTC
TCTTCTGGGAAAGAAGGAAGTGTGGCGAAATGCAGACAGATTTATCAAGAAGCCAACAGATCCATGAGACACTGCCAGGA
CAAAGAAGAGAGGCTTATGCTGTTGGAATCCTGGAGAAGTTTTGAAGGGGAGTTTGGAACCGTAGCAGACAAGGAGAGAG
TAGACAGACTCATGCCAGACGAGGTCAAGAAGAGAAGAAAGGTCCAGGCCGACGATGGTTCTGATGCCGGATGGCAAGAA
TACCGGGACTACATCTTTCCAGAGGATGCGGCCCAGCAGCCCAACCTCAAGCTTCTGGCCGTGGCCAAGCTGTGGAAGAA
ACAGCAACAGGAAAGAGAAGCTGCCGGACAGGATCCAGATAAGGACAGGAATGGGAGTGCACTTGCTGGTTAC

Alignment

ORF - retro_mmus_207 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASTAAGK-QRIPKVAKVKNKAPAEVQITAEQLLREAKERELELLPPPPQQKITDEEELNDYKLRKRKT
          MA.ST.A.K.QR.PKVA.VKNKA.AEVQITAEQLLREAKERELELL.PPPQQKITD.EE.NDYKLR.RK.
Retrocopy MASSTVAKKEQRLPKVAQVKNKAAAEVQITAEQLLREAKERELELLAPPPQQKITDAEEFNDYKLRRRKA

Parental  FEDNIRKNRTVISNWIKYAQWEESLKEIQRARSIYERALDVDYRNITLWLKYAEMEMKNRQVNHARNIWD
          FE.N.R..RTVISNWIKYAQWEESLKE..RARSIYERALDVDYRN.TLWLKYAEMEMKNRQVNHARNIWD
Retrocopy FEENLRQKRTVISNWIKYAQWEESLKELDRARSIYERALDVDYRNLTLWLKYAEMEMKNRQVNHARNIWD

Parental  RAITTLPRVNQFWYKYTYMEEMLGNVAGARQVFERWMEWQPEEQAWHSYINFELRYKEVERARTIYERFV
          RAITTLPRV.Q.WYKYTYMEE.LGNVAGARQVFERWMEWQPEEQAWHSYIN.ELRYKEVERARTIYERFV
Retrocopy RAITTLPRVKQLWYKYTYMEELLGNVAGARQVFERWMEWQPEEQAWHSYINLELRYKEVERARTIYERFV

Parental  LVHPAVKNWIKYARFEEKHAYFAHARKVYERAVEFFGDEHMDEHLYVAFAKFEENQKEFERVRVIYKYAL
          LVHPAVKNWIKYARFEE.HA..AHARKVYERAVEFFG.EHMD.HLYVAFAKFEENQKE.ERVRVIY.YAL
Retrocopy LVHPAVKNWIKYARFEERHASVAHARKVYERAVEFFGEEHMDQHLYVAFAKFEENQKELERVRVIYRYAL

Parental  DRISKQEAQELFKNYTIFEKKFGDRRGIEDIIVSKRRFQYEEEVKANPHNYDAWFDYLRLVESDAEADTV
          DRISKQEAQEL..NYTIFEKKFG.RR..E..IV.KRRF.YEEEVKANPHNYDAWFDYLRLVES.AEADTV
Retrocopy DRISKQEAQELLTNYTIFEKKFGERRDVEESIVRKRRFHYEEEVKANPHNYDAWFDYLRLVESEAEADTV

Parental  REVYERAIANVPPIQEKRHWKRYIYLWVNYALYEELEAKDPERTRQVYQASLELIPHKKFTFAKMWLYYA
          REVYERAIA.VPP..EKRHWKRYIYLWVNYALYEELEAKDPERTR.VYQASL.LIPH.KFTFAKMWLYYA
Retrocopy REVYERAIASVPPVLEKRHWKRYIYLWVNYALYEELEAKDPERTRRVYQASLQLIPHTKFTFAKMWLYYA

Parental  QFEIRQKNLPFARRALGTSIGKCPKNKLFKGYIELELQLREFDRCRKLYEKFLEFGPENCTSWIKFAELE
          QFEIRQKNLP.ARRALGTS.GKCPKNKLFKGYI.LELQLREFDRCRKLYEKFLEFGPENCTSWIKFAELE
Retrocopy QFEIRQKNLPLARRALGTSLGKCPKNKLFKGYIALELQLREFDRCRKLYEKFLEFGPENCTSWIKFAELE

Parental  TILGDIERARAIYELAISQPRLDMPEVLWKSYIDFEIEQEETERTRNLYRQLLQRTQHVKVWISFAQFEL
          TILGD.ERARAIYELAISQPRLDMPE.LWKSYIDFE.EQEE.ERTRNLYR.LLQRTQHVKVWIS.AQFE.
Retrocopy TILGDVERARAIYELAISQPRLDMPELLWKSYIDFEMEQEEPERTRNLYRRLLQRTQHVKVWISLAQFEF

Parental  SSGKEGSVAKCRQIYEEANKTMRNCEEKEERLMLLESWRSFEDEFGTVSDKERVDKLMPEKVKKRRKVQA
          SSGKEGSVAKCRQIY.EAN..MR.C..KEERLMLLESWRSFE.EFGTV.DKERVD.LMP..VKKRRKVQA
Retrocopy SSGKEGSVAKCRQIYQEANRSMRHCQDKEERLMLLESWRSFEGEFGTVADKERVDRLMPDEVKKRRKVQA

Parental  DDGSDAGWEEYYDYIFPEDAANQPNLKLLAMAKLWKKQQQEREAAEQDPDKDIDESESSSF
          DDGSDAGW.EY.DYIFPEDAA.QPNLKLLA.AKLWKKQQQEREAA.QDPDKD...S.....
Retrocopy DDGSDAGWQEYRDYIFPEDAAQQPNLKLLAVAKLWKKQQQEREAAGQDPDKDRNGSALAGY

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	15.30 RPM
SRP007412_cerebellum	0.00 RPM	19.93 RPM
SRP007412_heart	0.00 RPM	19.74 RPM
SRP007412_kidney	0.00 RPM	20.44 RPM
SRP007412_liver	0.00 RPM	14.53 RPM
SRP007412_testis	0.00 RPM	42.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_207 was not detected

EST

No EST(s) were mapped for retro_mmus_207 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_123203	1038 libraries	26 libraries	8 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_207 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_207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_207 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000012167	1 retrocopy	retro_meug_44,
Myotis lucifugus	ENSMLUG00000016513	1 retrocopy	retro_mluc_1434,
Mus musculus	ENSMUSG00000001767	1 retrocopy	retro_mmus_207 ,
Rattus norvegicus	ENSRNOG00000010587	1 retrocopy	retro_rnor_2345,