RetrogeneDB ID: retro_mmus_3096

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:140992582..140993173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nubpl
• Ensembl ID: ENSMUSG00000035142
• Aliases: None
• Description: nucleotide binding protein-like [Source:MGI Symbol;Acc:MGI:1924076]

Sequence

>retro_mmus_3096
CCAGAATTATCACCAAATAACTTAATGAGGCCTCTTTTGAACTATGGTATTGCTTGTATGTCAATGGGCTTTTTGGTTGA
AGAGACTGCGCCACTTGTTTGGAGAGGCCTTATGGTAATGTCAGCCATTGAGAAATTATTGAGACAGGTTGACTGGGGTC
AGCTGGACTCTTTAGTTGTGGACATGCCACCAGGAGCAGGAGATGTGCAGTTGTCAGTTTCACAGAATATCCCCATTTCA
GGTGCTGTGATTGTCTCCACACCTCAGGACATTGCACTAATGAATGCACACAAGGGTGTGGAGATGTTTCGGAAAGTCAA
TGTGCCTGTTCTTGGTCTTGTCCAAAACATGAGTGTCTTCCAGTGTCCAAAATGTAAACACAAAACTCATATTTTTGGTG
CTGATGGTGCAAGAAAACTAGCACAGACCCTTGATCTTGGTGTTCTAGGAGATGTTCCCTTGCACCTCAGTATAAGGGAA
GCTTCGGATATGGGTCAACCAGTTGTCTTTTCTCAGCCTGGAAGTGATGAGGCCAAAGCTTACTTGCATATTGCTTCAGA
AGTGGTGAGAAGATTGAAATCATCTCCAGAA

Alignment

ORF - retro_mmus_3096 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.46 %
• Parental protein coverage: 61.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PELSPNNLMRPLLNYGIACMSMGFLVEETAPLVWRGLMVMSAIEKLLRQVDWGQLDYLVVDMPPGTGDVQ
          PELSPNNLMRPLLNYGIACMSMGFLVEETAPLVWRGLMVMSAIEKLLRQVDWGQLD.LVVDMPPG.GDVQ
Retrocopy PELSPNNLMRPLLNYGIACMSMGFLVEETAPLVWRGLMVMSAIEKLLRQVDWGQLDSLVVDMPPGAGDVQ

Parental  LSVSQNIPISGAVIVSTPQDIALMDAHKGAEMFRKVNVPVLGLVQNMSVFQCPKCKHKTHIFGADGARKL
          LSVSQNIPISGAVIVSTPQDIALM.AHKG.EMFRKVNVPVLGLVQNMSVFQCPKCKHKTHIFGADGARKL
Retrocopy LSVSQNIPISGAVIVSTPQDIALMNAHKGVEMFRKVNVPVLGLVQNMSVFQCPKCKHKTHIFGADGARKL

Parental  AQTLDLDVLGDVPLHLSIREASDMGQPVVFSQPGSDEAKAYLHIASEVVRRLKSSPE
          AQTLDL.VLGDVPLHLSIREASDMGQPVVFSQPGSDEAKAYLHIASEVVRRLKSSPE
Retrocopy AQTLDLGVLGDVPLHLSIREASDMGQPVVFSQPGSDEAKAYLHIASEVVRRLKSSPE

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	3.46 RPM
SRP007412_cerebellum	0.00 RPM	2.13 RPM
SRP007412_heart	0.00 RPM	6.63 RPM
SRP007412_kidney	0.00 RPM	11.28 RPM
SRP007412_liver	0.00 RPM	8.90 RPM
SRP007412_testis	0.05 RPM	5.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3096 was not detected

EST

No EST(s) were mapped for retro_mmus_3096 retrocopy.

TSS

No TSS is located nearby retro_mmus_3096 retrocopy 5' end.

Lab

retro_mmus_3096 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3096 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000035142	1 retrocopy	retro_mmus_3096 ,
Xenopus tropicalis	ENSXETG00000014129	1 retrocopy	retro_xtro_69,