RetrogeneDB ID: retro_mmus_3319

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:18289119..18289784(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arl14ep
• Ensembl ID: ENSMUSG00000027122
• Aliases: Arl14ep, 2700007P21Rik, 4930448O08Rik, ARF7EP
• Description: ADP-ribosylation factor-like 14 effector protein [Source:MGI Symbol;Acc:MGI:1926020]

Sequence

>retro_mmus_3319
AAAGTTGTCATCAAAAATGACATGTTTTCACTTCAGCTTAGAACTGGAATGATACATTCTGGGAATAATACAATTTGTCT
CCATCATGTAAAAATGTATATTGACAGATTTGAAGAGTTGCAGAAATTACTTGTGACTCATTTAACTTACACAAGAAGCT
AGCTCAAAAGAATCTGCATGTAACTGACTTAGATGATGTCACTTTTATGAGCACAAAGTTTGGGGGACAATTCGTACCTG
GTTGAAAGCTTTGTCCAAAATGTACCCAGATTACCAATGGAAGTGTGGATGTTGATTCAGATGACCGCCAGAGATGGAAA
CCCGAGTCAGATGGAAGGACTGCTAAAGCTCTGAGGTCACTACAGTTTACAAACCCAGGAAAGCAAACTGAATTTGCTTT
GAAAAGTGGTAAAAGTGAGAAAAGAAAGCTCACCAAAAATTCATGCACTGCTTCTAACAGACAAATTATTCCAGCAAAGA
GTACTGTGTATGACTGCCAGGGCCTACTGATCTTCAGTGGCATGAACCCCTGTGACTGCCTGGACATGGACTGCTTGGGA
TGTTTCTATGCCTGCCCTACTTATAGCTCTACCAAATGTGGTGCTGAGTGCCACTGCAACCGCAAGTGGCTATATGAGCA
GAGAGAGTTTGTAGGAGGAGAGATG

Alignment

ORF - retro_mmus_3319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.48 %
• Parental protein coverage: 80.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KELSSNDMLLLQLRTGMTLSGNNTICLHHVKIYIDRFEDLQKSC-CDPFNIHKKLAKKNLHVIDLDDATF
          K....NDM..LQLRTGM..SGNNTICLHHVK.YIDRFE.LQK...CD.FN.HKKLA.KNLHV.DLDD.TF
Retrocopy KVVIKNDMFSLQLRTGMIHSGNNTICLHHVKMYIDRFEELQKLL<CDSFNLHKKLAQKNLHVTDLDDVTF

Parental  LSAKFGRQLVPGWKLCPKCTQIINGSVDVDSDDRQRRKPDSDGRTAKALRSLQFTNPGKQTEFAPEGGKR
          .S.KFG.Q.VPG.KLCPKCTQI.NGSVDVDSDDRQR.KP.SDGRTAKALRSLQFTNPGKQTEFA...GK.
Retrocopy MSTKFGGQFVPG*KLCPKCTQITNGSVDVDSDDRQRWKPESDGRTAKALRSLQFTNPGKQTEFALKSGKS

Parental  EKRKLTKATSAASDRQIIPAKSKVYDSQGLLIFSGMDLCDCLDEDCLGCFYACPTCGSTKCGAECRCDRK
          EKRKLTK....AS.RQIIPAKS.VYD.QGLLIFSGM..CDCLD.DCLGCFYACPT..STKCGAEC.C.RK
Retrocopy EKRKLTKNSCTASNRQIIPAKSTVYDCQGLLIFSGMNPCDCLDMDCLGCFYACPTYSSTKCGAECHCNRK

Parental  WLYEQIEIEGGEI
          WLYEQ.E..GGE.
Retrocopy WLYEQREFVGGEM

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	0.02 RPM	31.80 RPM
SRP007412_cerebellum	0.00 RPM	28.57 RPM
SRP007412_heart	0.00 RPM	8.97 RPM
SRP007412_kidney	0.00 RPM	16.21 RPM
SRP007412_liver	0.00 RPM	11.77 RPM
SRP007412_testis	0.00 RPM	21.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3319 was not detected

EST

No EST(s) were mapped for retro_mmus_3319 retrocopy.

TSS

No TSS is located nearby retro_mmus_3319 retrocopy 5' end.

Lab

retro_mmus_3319 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3319 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012417	1 retrocopy	retro_btau_1266,
Choloepus hoffmanni	ENSCHOG00000012698	1 retrocopy	retro_chof_1155,
Felis catus	ENSFCAG00000028620	1 retrocopy	retro_fcat_437,
Microcebus murinus	ENSMICG00000011547	2 retrocopies	retro_mmur_1003, retro_mmur_131,
Macaca mulatta	ENSMMUG00000017590	2 retrocopies	retro_mmul_1793, retro_mmul_984,
Mus musculus	ENSMUSG00000027122	1 retrocopy	retro_mmus_3319 ,
Mus musculus	ENSMUSG00000073568	1 retrocopy	retro_mmus_3320,