RetrogeneDB ID: retro_mmus_3100

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:4641464..4642854(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Stk38l
• Ensembl ID: ENSMUSG00000001630
• Aliases: Stk38l, 4930473A22Rik, B230328I19, Ndr2, Ndr54
• Description: serine/threonine kinase 38 like [Source:MGI Symbol;Acc:MGI:1922250]

Sequence

>retro_mmus_3100
ATGGCAATGATGGCAGGGGCAACAATTACCTTTCCTATGAGCAACCATACCCGGGAAAGAGTAACTGTGGCCAAGCTCAC
ACTGGAGAATTTTTACAGCAACCTAATTTTACAGCACGAAGAGAGAGAAACGAGGCAGAAGAAGTTAGAAGTGGCTATGG
AAGAAGAAGGACTGGCAGATGAGGAGAAAACGTTACGTCGATCGCAGCATGCTCATAAAGAAACAGTTCTTACGCCTTAA
GAGGACCAGACTTGGCCTGGATGACTTTGAGTCTCTGAAGGTTATAGGAAGAGGAGCTTTCGGAGAGGTGCGGCTGGTCC
AGAAGAAAGACAAGGGGCACATCTGTGCCATGAAGATCCTGAGGAAAGCTGACATGCTTGAGAAAGAGCAGGTGGCTCAT
ATCCGAGCAGAAAGGGACATTTTGGTGGAAGCAGATGGAGCCTGGGTGGTAAAGATATTCTACAGTTTTCAGGACAAACG
GAATCTCTATCTCATCATGGAATTTCTTCCTGGAGGTGACATGATGACATTGCTGATGAAGAAGGACACCTTAACAGAAT
AGGAGACACAGTTCTACATCTCAGAGACTGTCTTGACGATAGATGCAATTCACCAGCTGGGCTTCATCCACCGGGACATC
AAACCAGACATCCTTTTACTGGATGCCAAGGGACATGTAAAGTTATCCGATGTTGGTTTGTGCACGGGGTTAAAGAAAGC
TCACAGGACTGGATTCTACAGAAACCTCACACATAACCCACCAAGCAACTTCTCATTTCAGAACATGAATTCAAAGTGGA
AAGTAGAGACATGGAAGAAGAACAGGAGACAGCTGGCTTACTCCACAGTTGGAACACCAGACTACATTGCTCCAGAAGTA
TTCATGCAGACTGGCTACAACAAATTGTGTGACTGGTGGTCCTTGGGAGTGATTATGTACGAGATGCTAATAGGCTTTCC
ACCTTTCTGCTCCGAAACACCACAAGAAATGTACAGAAAAGTTATGAGCTGGAAGGAGACGCTGGCATTTCCTCCGGAAG
TGCCCGTCTCTGAGAAAGCCAAGGACTTGATTCTCAGATTTTGTACTGATTCTGAAGACAGAATTGGGAAAGGTGGTGTG
GAAGAAATCAGAGGTCATCCGTTCTTTGAGGGTGTAGACTGGGGGCACATAAGGGAAAGACCAGCAGCTATTCCTATAGA
AATCCGGAGTATAGATGACACCTCAAACTTTGATGACTTCCCTGAGTCTGATATCTTACAGCCAGTGCCGAATACCACAG
AGCCCGACTACAAATCCAAAGACCGGGTTTTTCTCAATTACACCTACAAAAGGTTTGAAGGGCTGACCCAGAGAGGCTCC
ATTCCTACATACATGAACGCTGGGAAGTTA

Alignment

ORF - retro_mmus_3100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMTAGATTTFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLADEEKKLRRSQH
          MAM.AGAT.TFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLAD.E.K..R...
Retrocopy MAMMAGATITFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLAD-EEKTLRRSQ

Parental  ARKET-EFLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKDTGHIYAMKILRKADMLEKEQVAHIRAER
          .......FLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKD.GHI.AMKILRKADMLEKEQVAHIRAER
Retrocopy HAHKE>QFLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKDKGHICAMKILRKADMLEKEQVAHIRAER

Parental  DILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAIDAIHQLGF
          DILVEADGAWVVK.FYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTE.ETQFYISETVL.IDAIHQLGF
Retrocopy DILVEADGAWVVKIFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTE*ETQFYISETVLTIDAIHQLGF

Parental  IHRDVKPDNLLLDAKGHVKLSDFGLCTGLKKAHRTEFYRNLTHNPPSDFSFQNMNSKRKAETWKKNRRQL
          IHRD.KPD.LLLDAKGHVKLSD.GLCTGLKKAHRT.FYRNLTHNPPS.FSFQNMNSK.K.ETWKKNRRQL
Retrocopy IHRDIKPDILLLDAKGHVKLSDVGLCTGLKKAHRTGFYRNLTHNPPSNFSFQNMNSKWKVETWKKNRRQL

Parental  AYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIGFPPFCSETPQETYRKVMSWKETLAFPPEVP
          AYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIGFPPFCSETPQE.YRKVMSWKETLAFPPEVP
Retrocopy AYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIGFPPFCSETPQEMYRKVMSWKETLAFPPEVP

Parental  VSEKAKDLILRFCTDSENRIGNGGVEEIKGHPFFEGVDWGHIRERPAAIPIEIRSIDDTSNFDDFPESDI
          VSEKAKDLILRFCTDSE.RIG.GGVEEI.GHPFFEGVDWGHIRERPAAIPIEIRSIDDTSNFDDFPESDI
Retrocopy VSEKAKDLILRFCTDSEDRIGKGGVEEIRGHPFFEGVDWGHIRERPAAIPIEIRSIDDTSNFDDFPESDI

Parental  LQPVPNTTEPDYKSKDWVFLNYTYKRFEGLTQRGSIPTYMKAGKL
          LQPVPNTTEPDYKSKD.VFLNYTYKRFEGLTQRGSIPTYM.AGKL
Retrocopy LQPVPNTTEPDYKSKDRVFLNYTYKRFEGLTQRGSIPTYMNAGKL

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	25.30 RPM
SRP007412_cerebellum	0.04 RPM	21.97 RPM
SRP007412_heart	0.06 RPM	16.78 RPM
SRP007412_kidney	0.27 RPM	17.98 RPM
SRP007412_liver	0.05 RPM	16.28 RPM
SRP007412_testis	0.46 RPM	8.51 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3100 was not detected

EST

No EST(s) were mapped for retro_mmus_3100 retrocopy.

TSS

No TSS is located nearby retro_mmus_3100 retrocopy 5' end.

Lab

retro_mmus_3100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3100 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000025573	1 retrocopy	retro_dnov_1680,
Monodelphis domestica	ENSMODG00000016636	1 retrocopy	retro_mdom_1913,
Mus musculus	ENSMUSG00000001630	2 retrocopies	retro_mmus_3100 , retro_mmus_347,