RetrogeneDB ID: retro_mmus_2565

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:49552256..49553267(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083477
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nsfl1c
• Ensembl ID: ENSMUSG00000027455
• Aliases: Nsfl1c, Munc-18c, Stxbp3a, p47
• Description: NSFL1 (p97) cofactor (p47) [Source:MGI Symbol;Acc:MGI:3042273]

Sequence

>retro_mmus_2565
ATTAAGATTGCACTTGCAAGCTTTTATGAGGATGGAGGGGATGAAGACATTGTGACCATTTCACAAGCAACCCCAAGTTC
AGTGTCCAGAGGCACAGCTCCTAGTGATAATAGAGTGACATCCTTCAGAGACCTCTTTCATGACCAAGATGAAGAGGAAG
AGGAAGAGGAGGGACAGAGGTTTTATGCTGGGGGCTCAGAGAGAAGTGGACAGCAGATTGTTGGTCCTCCCCGGAAGAAA
AGTCCCAACGAGCTGGTGGATGATCTGTTTAAGGGTGCCAAAGAGCATGGGGCTGTAGCTGTGGAACGAGTGACCAAGAG
CCCTGGAGAGACCAGTAAACCGAGACCATTTGCAGGAGGGGGCTACCGCCTTGGAGCAGCACTAGAGGAAGAGTCTGCCT
ATGTGGCAGGAGAAAGGAGGTGGCATTCAGGGCAGGATGTTCATGTAGTGCTAAAGCTCTGGAAAACTGGATTCAGCCTA
GACAATGGTGACCTTAGAAGCTACCAAGACCCATCCAATGCCCCGTTTCTGGAGTCTATCCGTAGAGGGGAGGTTCCTGC
AGAGCTTCAGAGGTTAGCGCATGGTGGGCAGGTGAACCTGGATATGGAGGATCATCGGGATGAGGACTTCATGAAGCCCA
AGGGAGCTTTCAAAGCCTTCACTGGCAAGGGCCAGAAACTGAGCAGCATGGCCCCCCAGGTATTAAACACCAGCTCTCCA
GCCCAACAAGCTGAAAATGAAGCCAAAGCTAGCTCGTCCATCTTAATCAATGAAGCAGAACCTACCACGGACATCCAAAT
CCGGCTCGCAGATGGCGAGAGGCTGGTGCAGAAATTCAACCACAGCCACAGGATCAGCGACATCCGGCTCTTCATCGTGG
ATGCCCGGCCAGCTATGGCTGCCACCAGTTTTGTCCTTATGACTACCTTCCCTAACAAAGAGCTGGCTGATGAGAACCAA
ACCCTGAAGGAAGCCAACCTTCTCAACGCTGTCATCGTGCAGCGGTTAACA

Alignment

ORF - retro_mmus_2565 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.47 %
• Parental protein coverage: 91.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQIALASFYEDGGDEDIVTISQATPSSVSRGTAPSDNRVTSFRDLIHDQDEEEEEEEGQRFYAGGSERSG
          ..IALASFYEDGGDEDIVTISQATPSSVSRGTAPSDNRVTSFRDL.HD.........GQRFYAGGSERSG
Retrocopy IKIALASFYEDGGDEDIVTISQATPSSVSRGTAPSDNRVTSFRDLFHDXXXXXXXXXGQRFYAGGSERSG

Parental  QQIVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAAPEEESAYVAGERR
          QQIVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAA.EEESAYVAGERR
Retrocopy QQIVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSPGETSKPRPFAGGGYRLGAALEEESAYVAGERR

Parental  RHSGQDVHVVLKLWKTGFSLDNGDLRSYQDPSNAQFLESIRRGEVPAELRRLAHGGQVNLDMEDHRDEDF
          .HSGQDVHVVLKLWKTGFSLDNGDLRSYQDPSNA.FLESIRRGEVPAEL.RLAHGGQVNLDMEDHRDEDF
Retrocopy WHSGQDVHVVLKLWKTGFSLDNGDLRSYQDPSNAPFLESIRRGEVPAELQRLAHGGQVNLDMEDHRDEDF

Parental  VKPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENEAKASSSILINEAEPTTNIQIRLADGGRLVQKFN
          .KPKGAFKAFTG.GQKL.S.APQVLNTSSPAQQAENEAKASSSILINEAEPTT.IQIRLADG.RLVQKFN
Retrocopy MKPKGAFKAFTGKGQKLSSMAPQVLNTSSPAQQAENEAKASSSILINEAEPTTDIQIRLADGERLVQKFN

Parental  HSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIVQRLT
          HSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIVQRLT
Retrocopy HSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIVQRLT

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	0.14 RPM	45.25 RPM
SRP007412_cerebellum	0.13 RPM	59.18 RPM
SRP007412_heart	0.12 RPM	48.16 RPM
SRP007412_kidney	0.27 RPM	58.71 RPM
SRP007412_liver	0.08 RPM	32.66 RPM
SRP007412_testis	0.14 RPM	20.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2565 was not detected

EST

No EST(s) were mapped for retro_mmus_2565 retrocopy.

TSS

No TSS is located nearby retro_mmus_2565 retrocopy 5' end.

Lab

retro_mmus_2565 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2565 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088833	1 retrocopy	retro_hsap_4050,
Gorilla gorilla	ENSGGOG00000013539	1 retrocopy	retro_ggor_2718,
Macropus eugenii	ENSMEUG00000003940	2 retrocopies	retro_meug_1890, retro_meug_605,
Macaca mulatta	ENSMMUG00000015994	1 retrocopy	retro_mmul_2337,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Mus musculus	ENSMUSG00000027455	1 retrocopy	retro_mmus_2565 ,
Nomascus leucogenys	ENSNLEG00000009341	1 retrocopy	retro_nleu_2800,
Otolemur garnettii	ENSOGAG00000002630	2 retrocopies	retro_ogar_1144, retro_ogar_1609,
Pongo abelii	ENSPPYG00000010851	1 retrocopy	retro_pabe_3324,
Pan troglodytes	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745,