RetrogeneDB ID: retro_mmus_2774

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:110378321..110378628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dtd1
• Ensembl ID: ENSMUSG00000027430
• Aliases: Dtd1, 0610006H08Rik, DUE-B, Hars2
• Description: D-tyrosyl-tRNA deacylase 1 [Source:MGI Symbol;Acc:MGI:1913294]

Sequence

>retro_mmus_2774
GAGAGCTTCTACAATAGCCTCCTGGAGCAGCTGCACAAGAGCAGGTCACAGCTTATCAGAGATGGCAAGTTTGGTTCCTA
TACTCAAGTGCATGATCAGAAAGATGGACCTTGACTATAGAACGAGAGTTTCTGCTGCTAGGACTGCTAATGCTGACCAA
AAGCAACTGTCAAAGATAGAGAAACAGTAGCAGAGAAAAGACCAGAGGCAAGGCCCTTCTAAGTCAAGCAAAGAATATAA
TGAACCCCAAAAAGATGACCACAGCGTCAGCAGCAGGACAGAGGGTAATGTGATTTCTGAGCTGGAG

Alignment

ORF - retro_mmus_2774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.04 %
• Parental protein coverage: 50.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESFYNSFLEQLRKSYRPELIRDGKFGAYMQVHIQNDGP-VTIELE-SPAPGAASSDPKQLSKLEKQQQRK
          ESFYNS.LEQL.KS.R..LIRDGKFG.Y.QVH.Q.DGP..TIE.E...A...A..D.KQLSK.EKQ.QRK
Retrocopy ESFYNSLLEQLHKS-RSQLIRDGKFGSYTQVHDQKDGP<LTIERE<VSAARTANADQKQLSKIEKQ*QRK

Parental  EKTRAKGPSESSKERNAPRKEDRSASSGAEGDVSSERE
          ......GPS.SSKE.N.P.K.D.S.SS..EG.V.SE.E
Retrocopy D--QRQGPSKSSKEYNEPQKDDHSVSSRTEGNVISELE

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	36.17 RPM
SRP007412_cerebellum	0.00 RPM	35.48 RPM
SRP007412_heart	0.00 RPM	9.68 RPM
SRP007412_kidney	0.00 RPM	16.86 RPM
SRP007412_liver	0.00 RPM	8.47 RPM
SRP007412_testis	0.00 RPM	14.54 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2774 was not detected

EST

No EST(s) were mapped for retro_mmus_2774 retrocopy.

TSS

No TSS is located nearby retro_mmus_2774 retrocopy 5' end.

Lab

retro_mmus_2774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2774 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008964	1 retrocopy	retro_btau_767,
Macropus eugenii	ENSMEUG00000009170	2 retrocopies	retro_meug_137, retro_meug_1809,
Macaca mulatta	ENSMMUG00000012880	1 retrocopy	retro_mmul_217,
Monodelphis domestica	ENSMODG00000005696	1 retrocopy	retro_mdom_509,
Mus musculus	ENSMUSG00000027430	1 retrocopy	retro_mmus_2774 ,
Oryctolagus cuniculus	ENSOCUG00000010988	1 retrocopy	retro_ocun_1357,
Tupaia belangeri	ENSTBEG00000000242	1 retrocopy	retro_tbel_3434,