RetrogeneDB ID: retro_mmus_1734

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:66417445..66417800(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Trappc6b
• Ensembl ID: ENSMUSG00000020993
• Aliases: Trappc6b, 5830498C14Rik, C79212
• Description: trafficking protein particle complex 6B [Source:MGI Symbol;Acc:MGI:1925482]

Sequence

>retro_mmus_1734
TTTCAAGTGGGACAAAGATTGATAGGAAGGTTTACCGAAGATACTGCGAGATTCAAGGATGCATTAGAAATCATAAAGAT
CATATGTAAAGATTTTTGGACTACAGTATTCAAGAAATAAATTGGCCATCTAAGGACAAATCATCAGGGTGTGTATGTCC
TTGAGGACAACAAATTTTGACTACTTAACTCGTCTGTAAGCAGGAAAAGAGTATTCAGAGCATGCATCAAAGTATCTAGC
ATTTACATGTAGCTTAATCAGAGGTGGCTTGTCAACCTTGGGAATAGAAAGTAGGGTAATACCTGAAGCATCTTCAGTGC
CTGCCTGCAAGCTTCAGATGATGACACAGAGGCTG

Alignment

ORF - retro_mmus_1734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.11 %
• Parental protein coverage: 74.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FRVGQGLIERFTKDTARFKDELDIMKFICKDFWTTVFKKQIDNLRTNHQGIYVLQDNKFRL-LIQLSAGK
          F.VGQ.LI.RFT.DTARFKD.L.I.K.ICKDFWTTVFKK.I..LRTNHQG.YVL.DNKF.L.L..L.AGK
Retrocopy FQVGQRLIGRFTEDTARFKDALEIIKIICKDFWTTVFKK*IGHLRTNHQGVYVLEDNKF*L>LTRL*AGK

Parental  QYLEHASKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQKL
          .Y.EHASKYLAFTC.LIRGGLS.LGI.S.V..E.SS.PACK.Q.M.Q.L
Retrocopy EYSEHASKYLAFTCSLIRGGLSTLGIESRVIPEASSVPACKLQMMTQRL

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	46.28 RPM
SRP007412_cerebellum	0.00 RPM	38.91 RPM
SRP007412_heart	0.00 RPM	29.64 RPM
SRP007412_kidney	0.00 RPM	47.14 RPM
SRP007412_liver	0.00 RPM	22.72 RPM
SRP007412_testis	0.00 RPM	28.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1734 was not detected

EST

No EST(s) were mapped for retro_mmus_1734 retrocopy.

TSS

No TSS is located nearby retro_mmus_1734 retrocopy 5' end.

Lab

retro_mmus_1734 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1734 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013828	1 retrocopy	retro_etel_1104,
Myotis lucifugus	ENSMLUG00000002627	2 retrocopies	retro_mluc_1179, retro_mluc_663,
Mus musculus	ENSMUSG00000020993	2 retrocopies	retro_mmus_1734 , retro_mmus_2069,
Oryctolagus cuniculus	ENSOCUG00000002171	1 retrocopy	retro_ocun_813,
Sarcophilus harrisii	ENSSHAG00000001400	1 retrocopy	retro_shar_235,
Ictidomys tridecemlineatus	ENSSTOG00000002897	2 retrocopies	retro_itri_476, retro_itri_795,
Tupaia belangeri	ENSTBEG00000003331	1 retrocopy	retro_tbel_4529,