RetrogeneDB ID: retro_mmus_2653

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:55722772..55723201(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tiprl
• Ensembl ID: ENSMUSG00000040843
• Aliases: Tiprl, 1810011K17Rik
• Description: TIP41, TOR signalling pathway regulator-like (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1915087]

Sequence

>retro_mmus_2653
TGTGTGAACAACTACTAGGGCATGCTCAAAGCAGCTTGTGCTGAATAGTGACAAGAAAGTAGGACGGAGGGTGAACACTC
CGAAGAAGTTATTAAACTGGATGACTGGACCTATACAACAGAATAGAAAGAAACGTTGCTTGGAGAATCCTTAAGTTAAA
GGTTGTACCTACAACAGATAGTATAGATACAGAAAAATCGAAAGCCAAAGAACAGATTAAAATTTTTAAAGAAGTTCTCC
TGTTTGAAGATGAATTGCACGATCACGGCGTTTCCAGCCTGGGTGTGAAAATTAAAGTAACGCCTTCCAGTTTTTTCTGC
TATTGCATTTGTCTTGAGAATTGATGGGGTGCTCATCAGAATGAATGACAGAAGGCTTTGCCATGAGGCTGGCAAAACTT
ACATGTTATGAGAATATACATCCAGAGAG

Alignment

ORF - retro_mmus_2653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 53.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CVNNYQGMLKVACAEEWQESRTEGEHSKEVIKPYDWTYTTDYKGTLLGESL-KLKVVPTTDHIDTEKLKA
          CVNNY.GMLK.ACAE..QESRTEGEHS.EVIK..DWTYTT..K.TLLGESL.KLKVVPTTD.IDTEK.KA
Retrocopy CVNNY*GMLKAACAE**QESRTEGEHSEEVIKLDDWTYTTE*KETLLGESL<KLKVVPTTDSIDTEKSKA

Parental  REQIKFFEEVLLFEDELHDHGVSSLSVKIRVMPSS-FFLLLR-FFLRIDGVLIRMNDTRLYHEADKTYML
          .EQIK.F.EVLLFEDELHDHGVSSL.VKI.V.PSS.FFLLL..F.LRIDGVLIRMND.RL.HEA.KTYML
Retrocopy KEQIKIFKEVLLFEDELHDHGVSSLGVKIKVTPSS<FFLLLH<FVLRIDGVLIRMNDRRLCHEAGKTYML

Parental  REYTSRE
          .EYTSRE
Retrocopy *EYTSRE

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	38.60 RPM
SRP007412_cerebellum	0.00 RPM	24.79 RPM
SRP007412_heart	0.00 RPM	19.71 RPM
SRP007412_kidney	0.00 RPM	23.25 RPM
SRP007412_liver	0.00 RPM	13.68 RPM
SRP007412_testis	0.00 RPM	44.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2653 was not detected

EST

No EST(s) were mapped for retro_mmus_2653 retrocopy.

TSS

No TSS is located nearby retro_mmus_2653 retrocopy 5' end.

Lab

retro_mmus_2653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2653 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008689	3 retrocopies	retro_chof_1079, retro_chof_1094, retro_chof_1746,
Cavia porcellus	ENSCPOG00000009945	1 retrocopy	retro_cpor_763,
Echinops telfairi	ENSETEG00000005808	1 retrocopy	retro_etel_1273,
Microcebus murinus	ENSMICG00000007808	1 retrocopy	retro_mmur_1335,
Myotis lucifugus	ENSMLUG00000011927	3 retrocopies	retro_mluc_607, retro_mluc_909, retro_mluc_941,
Monodelphis domestica	ENSMODG00000002880	1 retrocopy	retro_mdom_180,
Mus musculus	ENSMUSG00000040843	1 retrocopy	retro_mmus_2653 ,
Ochotona princeps	ENSOPRG00000011313	1 retrocopy	retro_opri_885,
Pteropus vampyrus	ENSPVAG00000005071	1 retrocopy	retro_pvam_257,
Rattus norvegicus	ENSRNOG00000003048	1 retrocopy	retro_rnor_2197,
Sarcophilus harrisii	ENSSHAG00000018932	1 retrocopy	retro_shar_771,
Ictidomys tridecemlineatus	ENSSTOG00000014921	1 retrocopy	retro_itri_1756,
Tupaia belangeri	ENSTBEG00000017081	3 retrocopies	retro_tbel_1717, retro_tbel_2833, retro_tbel_3376,