RetrogeneDB ID: retro_mmus_1579

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:54002339..54003329(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Epb4.1l4b
• Ensembl ID: ENSMUSG00000028434
• Aliases: Epb4.1l4b, 6430543G08Rik, AA589614, AU021054, BB007528, D4Ertd346e, Ehm2, Epb41l4b, Lulu2
• Description: erythrocyte protein band 4.1-like 4b [Source:MGI Symbol;Acc:MGI:1859149]

Sequence

>retro_mmus_1579
GAATTGAAGTGCCCCTATGAAATGGTGTGGGACTAGCTGTCCTCTTTCTGCAAGCGGAGCTAGGAGAGTGTGAGCTCCTG
GAACACACATCTGAGCTTGTGTCTGAGTTTCGGTTCCTCCCAAATCAGACAGAAGCCATGGAGTTCGATATCTTCAAGAG
ATGGAAAGAGTACAGGGGAAAGAGCCCTGCCCAGGCAGAACTCTCCCATCTGAACAAAGCGAAGTGGCTGGAAATGTATG
GGGTGGACATGCATGTTGTCAGTGGAAGAGATGGCTGTGAATATTCTCTTGGACTGACCCCGACAGGCATATTAATCTTA
GAAGGAGCTAACAAAATATGCTTATTCTATTCGCCTAAGATCACCAAAATGGACTTTAAAAAAGAGCAAACTGACCCTCG
TAGTAGTGGAAGATGATGACCAGGGGCGTGAGCAAGAGCACACCTTCGTGTTCAGGCTGGACAGTGCGCGTACCTGTAAG
TACTTGTGGAAGTGTGCAGTGGAGCACTGTGCCTTCTGTCTGCGCACACCCATCAACAGCAAGTCCTCCAGATCTGACTT
CATCCGGCTGGGTTCCCACTTCCGGTTCAGTGGACAGTCGCAATATCAAGCTGCACACGGCTCCAGATTGCGAAGAACCT
TTGAGCCTAGCAAACGTTACCCATCCCGGCAACATTCCACATTCAAAGCCAGCAACCCAGTGATTGCTGCTCAGTTCTGC
TCTAAAACAAATCTTGAAGTCCATAATTACCAGCCTCAGTACCTTCGTGACGTCCACCCCAGCCAGCCCCGGTGGCGCCC
TCACTCTCCAAATGTCAGTAACCATTCCATCTGCAAGTAAAACAAGCCATGTTTTCAGGATGACAGGCCACACTGGAAAG
CCTCAGCCAGTGGAGATGGCAGCCACTTTGACTATGTCCAGGACCAGAACCAGAGGAACTTAGGAGAGGCGTACAATGTC
ACGTACCGGGACAAACTCATGACCGCACTC

Alignment

ORF - retro_mmus_1579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.24 %
• Parental protein coverage: 63.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLKCPYE-TAVELAALCLQAELGECELPEHTPELVSEFRFIPNQTEAMEFDIFQRWKEYRGKSPAQAELS
          .LKCPYE...V.LA.L.LQAELGECEL.EHT.ELVSEFRF.PNQTEAMEFDIF.RWKEYRGKSPAQAELS
Retrocopy ELKCPYE<NGVGLAVLFLQAELGECELLEHTSELVSEFRFLPNQTEAMEFDIFKRWKEYRGKSPAQAELS

Parental  YLNKAKWLEMYGVDMHVVRGRDGCEYSLGLTPTGILIFEGANKIGLFFWPKITKMDFKK-SKLTLVVVED
          .LNKAKWLEMYGVDMHVV.GRDGCEYSLGLTPTGILI.EGANKI.LF..PKITKMDFKK.SKLTLVVVED
Retrocopy HLNKAKWLEMYGVDMHVVSGRDGCEYSLGLTPTGILILEGANKICLFYSPKITKMDFKK>SKLTLVVVED

Parental  DDQGREQEHTFVFRLDSARTCKHLWKCAVEHHAFFRLRTPSNSKSARSDFIRLGSRFRFSGRTEYQATHG
          DDQGREQEHTFVFRLDSARTCK.LWKCAVEH.AF..LRTP.NSKS.RSDFIRLGS.FRFSG...YQA.HG
Retrocopy DDQGREQEHTFVFRLDSARTCKYLWKCAVEHCAFC-LRTPINSKSSRSDFIRLGSHFRFSGQSQYQAAHG

Parental  SRLRRTSTFERKPSKRYPSRRHSTFKASNPVIAAQLCSKANPEVHNYQPQYHPDVHPSQPRWRPHSPNVS
          SRLRRT..FE..PSKRYPSR.HSTFKASNPVIAAQ.CSK.N.EVHNYQPQY..DVHPSQPRWRPHSPNVS
Retrocopy SRLRRT--FE--PSKRYPSRQHSTFKASNPVIAAQFCSKTNLEVHNYQPQYLRDVHPSQPRWRPHSPNVS

Parental  NHSICKQNKPCFQDDRPHWKTSASGDGSHFDYVQDQNQRNLGGAYSVTYRDKLMTAL
          NHSICK.NKPCFQDDRPHWK.SASGDGSHFDYVQDQNQRNLG.AY.VTYRDKLMTAL
Retrocopy NHSICK*NKPCFQDDRPHWKASASGDGSHFDYVQDQNQRNLGEAYNVTYRDKLMTAL

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	50.72 RPM
SRP007412_cerebellum	0.04 RPM	81.15 RPM
SRP007412_heart	0.00 RPM	3.21 RPM
SRP007412_kidney	0.04 RPM	26.24 RPM
SRP007412_liver	0.00 RPM	102.32 RPM
SRP007412_testis	0.00 RPM	6.31 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1579 was not detected

EST

No EST(s) were mapped for retro_mmus_1579 retrocopy.

TSS

No TSS is located nearby retro_mmus_1579 retrocopy 5' end.

Lab

retro_mmus_1579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1579 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028434	1 retrocopy	retro_mmus_1579 ,