RetrogeneDB ID: retro_mmus_1627

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:22184766..22185579(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snx4
• Ensembl ID: ENSMUSG00000022808
• Aliases: Snx4, 1810036H14Rik, AI037066
• Description: sorting nexin 4 [Source:MGI Symbol;Acc:MGI:1916400]

Sequence

>retro_mmus_1627
TTCATTTTTAACCCAGGTAACTGGAAGGAGACTGTGAATGAGACTGGATTTCAGCTGAAGGCAGACTCCAGGTTAAAAGA
GCTTAATGCAACATTCAGAGTGAAGAACCCAGACAAGAGGTTTACTGAGCTGAGGCACTACAGTGATGAGCTGCAGTCTG
TCATCTCACATCTCCTTCGAGTCAGAGCTAGAGTAGCAGATCGACTCTATGGTGTATATAAAGTACATGGGAATTATGGG
AGAGTTTTTAGTGAATGGTGTGCCATCGAAAAAGAAATGGGGGATGGGCTGCAGAGTGCTGGGCATCACATGGACGTGTA
TGCATCTTCTATTGATGATATTTTGGAAGATGAAGAGCACTATGCAGATCAGCTGAAGGACTATATGTTTTATGCAGAAG
CACTTCGGGCTGTGTGCAGGAAGCATGAGCTTATGAAGTATGACCTGGAGACAGCTGCTCAAGACCTGACTGCCAAGAAG
CAGCAGTGCGAGGAGCTGGCCACTGGGACTATGAGAACATTCTCGTTGAAGGGAATGACTACCAAACTCTTTGGTCAAGA
AACTCCAGAGCAAAGAGAAACCAGGATAAAGGTTCTAGAGGAGCAGATAAATGAAGGGGAAGAGCAGCTGAAGTCTAAAA
ATCTGGGAGGCAGAGAATTTGTGAAAAATGCATGGGCTGATATTGAACGCTTCAAAGAACAAAAGAACCGGGACCTAAAG
GAAGCCCTCATCAGCTATGATGTCATGCAGATCAGCATGTGCAAAAAGAGAATTCAGGTTTGGACCAATGCTAAAGAATG
CTTCAGCAACATG

Alignment

ORF - retro_mmus_1627 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.73 %
• Parental protein coverage: 60.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLTQEGNWKETVNETGFQLKADSRLKALNATFRVKNPDKRFTELRHYSDELQSVISHLLRVRARVADRLY
          F....GNWKETVNETGFQLKADSRLK.LNATFRVKNPDKRFTELRHYSDELQSVISHLLRVRARVADRLY
Retrocopy FIFNPGNWKETVNETGFQLKADSRLKELNATFRVKNPDKRFTELRHYSDELQSVISHLLRVRARVADRLY

Parental  GVYKVHGNYGRVFSEWSAIEKEMGDGLQSAGHHMDVYASSIDDILEDEEHYADQLKEYLFYAEALRAVCR
          GVYKVHGNYGRVFSEW.AIEKEMGDGLQSAGHHMDVYASSIDDILEDEEHYADQLK.Y.FYAEALRAVCR
Retrocopy GVYKVHGNYGRVFSEWCAIEKEMGDGLQSAGHHMDVYASSIDDILEDEEHYADQLKDYMFYAEALRAVCR

Parental  KHELMQYDLETAAQDLAAKKQQCEELATGTVRTFSLKGMTTKLFGQETPEQREARIKVLEEQINEGEQQL
          KHELM.YDLETAAQDL.AKKQQCEELATGT.RTFSLKGMTTKLFGQETPEQRE.RIKVLEEQINEGE.QL
Retrocopy KHELMKYDLETAAQDLTAKKQQCEELATGTMRTFSLKGMTTKLFGQETPEQRETRIKVLEEQINEGEEQL

Parental  KSKNLEGREFVKNAWADIERFKEQKNRDLKEALISYAVMQISMCKKGIQVWTNAKECFSKM
          KSKNL.GREFVKNAWADIERFKEQKNRDLKEALISY.VMQISMCKK.IQVWTNAKECFS.M
Retrocopy KSKNLGGREFVKNAWADIERFKEQKNRDLKEALISYDVMQISMCKKRIQVWTNAKECFSNM

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	0.09 RPM	27.57 RPM
SRP007412_cerebellum	0.00 RPM	22.10 RPM
SRP007412_heart	0.00 RPM	28.33 RPM
SRP007412_kidney	0.06 RPM	40.60 RPM
SRP007412_liver	0.05 RPM	25.83 RPM
SRP007412_testis	0.09 RPM	35.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1627 was not detected

EST

No EST(s) were mapped for retro_mmus_1627 retrocopy.

TSS

No TSS is located nearby retro_mmus_1627 retrocopy 5' end.

Lab

retro_mmus_1627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1627 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022808	1 retrocopy	retro_mmus_1627 ,
Sarcophilus harrisii	ENSSHAG00000000917	1 retrocopy	retro_shar_818,
Tursiops truncatus	ENSTTRG00000014983	1 retrocopy	retro_ttru_398,