RetrogeneDB ID: retro_mmus_2239

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:38438963..38439795(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nudt22
• Ensembl ID: ENSMUSG00000037349
• Aliases: Nudt22, 0610006K04Rik, AI851793, AW545547
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 22 [Source:MGI Symbol;Acc:MGI:1915573]

Sequence

>retro_mmus_2239
ATGGACCCCGAGTTGTCCCTGCTGCTGCTGTGCCCTTTCTAGGGACTGTCCCAGGAACAGGTAGCAGCAGAGCTGAGCCC
AGCTCATGATCGTTGTCCATTGCCTGGAGGAGACAAGACCATCACTGTCATCTGGGAGACCCGGCTACAGGCCCAACCTT
GGATCTTTGATGCTCTCAGCTTCTGCCTTCACTCAGCCACACTGGTCTCCAGCTTACCTGAGCCACAGCTGCTCCCGCAT
CTGGGTCTAACTTCCTAGCAGGACTTCCCGGGCACCAACTGGTCCAGCTCAGCTTCCCGGCTGTGACAGCAGGGAGCTGC
AGATTAGGGTGACAAGCAAGCCTATCTGGCAGACCAGCTGGGGGTGGGTGCCACATTGGTCAGGGCTGATGACTTCCTTG
TCTTCCTGCGCTGCTCTCAGCAGGTAGCAGAAGCACCTGGACTGGGGGATGTGCCCGGTGGGCACCCTGAACCTCAAGTC
CTGTGCTCTGGTGGGATCCCCCAGCCACAAGGACCTCCCTGGGGAGCTGGTGGTCCGAAAGCTCTTCTCCAGTGTCCTAC
AGGAGATCTGTGATGAGGTGAACCTTCCATTGCACACCTTGAACCAGCCTCTGTCATTGGGTATCGCTTGCGATGAGAGC
AGCATGGGCAGAGCCAGTGCAGAGTTCTATGTCCAGTGCAGCCTGATTTCAGAGGTCAGGAGTTGTTACCTGAGTGGGGG
ACCTGAGGCCCACCAGTCTACAGGAATCGTCTTTGTGGAGACACAGAGGGTACAGAGACTGCAGAAAACAAAGATGTGGG
CACCACTCTGCCCCTCAGCCAAAGGCTCCATC

Alignment

ORF - retro_mmus_2239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.59 %
• Parental protein coverage: 90.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDPEVSLLLLCPLGGLSQEQVAVELSPAHDRRPLPGGDKAITAIWETRQQAQPWIFDAPKFRLHSATLVS
          MDPE.SLLLLCP..GLSQEQVA.ELSPAHDR.PLPGGDK.IT.IWETR.QAQPWIFDA..F.LHSATLVS
Retrocopy MDPELSLLLLCPF*GLSQEQVAAELSPAHDRCPLPGGDKTITVIWETRLQAQPWIFDALSFCLHSATLVS

Parental  SSPEPQLLLHLGLTSYRDFLGTNWSSSASWLRQQGAADWGDKQAYLADPLGVGAALVTADDFLVFLRRSQ
          S.PEPQLL.HLGLTS..DF.GTNWSSSAS.L.QQGAAD.GDKQAYLAD.LGVGA.LV.ADDFLVFLR.SQ
Retrocopy SLPEPQLLPHLGLTS*QDFPGTNWSSSASRL*QQGAAD*GDKQAYLADQLGVGATLVRADDFLVFLRCSQ

Parental  QVAEAPGLVDVPGGHPEPQALCSGGIPR-HKDLPGLLVVRELFSSVLQEICDEVNLPLHTLSQPLLLGIA
          QVAEAPGL.DVPGGHPEPQ.LCSGGIP..HKDLPG.LVVR.LFSSVLQEICDEVNLPLHTL.QPL.LGIA
Retrocopy QVAEAPGLGDVPGGHPEPQVLCSGGIPQ>HKDLPGELVVRKLFSSVLQEICDEVNLPLHTLNQPLSLGIA

Parental  CNETSAGRASAEFYVQCSLTSEEVRSYYLSGGPEAHESTGIIFVETQRVQRLQETEMWAQLCPSAKGAI
          C.E.S.GRASAEFYVQCSL.S.EVRS.YLSGGPEAH.STGI.FVETQRVQRLQ.T.MWA.LCPSAKG.I
Retrocopy CDESSMGRASAEFYVQCSLIS-EVRSCYLSGGPEAHQSTGIVFVETQRVQRLQKTKMWAPLCPSAKGSI

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	3.18 RPM
SRP007412_cerebellum	0.00 RPM	10.12 RPM
SRP007412_heart	0.00 RPM	11.27 RPM
SRP007412_kidney	0.00 RPM	9.66 RPM
SRP007412_liver	0.00 RPM	4.34 RPM
SRP007412_testis	0.00 RPM	1.60 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2239 was not detected

EST

No EST(s) were mapped for retro_mmus_2239 retrocopy.

TSS

No TSS is located nearby retro_mmus_2239 retrocopy 5' end.

Lab

retro_mmus_2239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2239 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000037349	1 retrocopy	retro_mmus_2239 ,