RetrogeneDB ID: retro_mmus_343

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:88932676..88933573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tldc1
• Ensembl ID: ENSMUSG00000034105
• Aliases: Tldc1, 4632415K11Rik, Kiaa1609
• Description: TBC/LysM associated domain containing 1 [Source:MGI Symbol;Acc:MGI:1921597]

Sequence

>retro_mmus_343
GCTGTGCAGGTGATGGCTGCACAGCTGCTCTCAGAGATGAAGTTTCAAGATGCCCACCAGTTTCTGGGCCTTCAGTGTTT
GGACCAGATCTGCGACCAAGCCATGATGGAGGAGTGGGTGTTCCATGTCCCTTGGGTGGGTGTGTTTCTGAGTGTGGTCA
TCCACAAGTGCCTATGCCTCCTGGGCCCATCCTTTGACCATTTCACACTGGTCCCCGAGTGCCACATGGACCAAGGAAGG
CCATTTGAGAGCATTCCAGATGTGCTGTCTGTCATCTACCTCAGCTCCCACCTGGCAGTGGAGCATCGGCAACTCTGGTG
CCTGCTGTTTTCCACACAGTTCCATGGGCAGAGCTTCTCCCAGCTATGCTGCCTCGTCACGAACCAGGGGCCCAGCCTGA
TTGTCCTTAAGGACAGGAATGGCTACGTCTTTGGTGGCTTTGCTTCCTGCTCTTGGGAAGTTAAGCCTCAGTTCCAAGGG
GACAACAAATGTTTCCTGTTCTCCATTGCCCCCCAGAATGGCCACACATCTGCACACGGCTACAATAACCACTTCATGTA
CTTAAATTATAGACAGCAGTCCATACCCAATGGACTGGGCATGGGTGGACAGCACCATTACTTTGGGCTTTGGGTGGTTG
CCGACTTTGGGAAAGGACACAGCAAGCCCAAGCCTGCATGCACCACCTACAACAGCACACAACTGTCTGCCCAGGAGGAC
TTCTTGTTTGATAATATGGAGGTGTGGGGACTTGGAGATATATATTTCTTAGAGATATATCAGGACAAGAACAGGAAGAG
CATCCTAGACTCAAATCCTGACGTCCATAGCCTGTTGGAGATCAGTAGATGGATTTGACACAGTGAGGGTCTGCAGGAAG
TTCCCAAGGATGAGGAT

Alignment

ORF - retro_mmus_343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 65.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SMQAMVAQLLSEMKFQDGYKFQGPQCLDQVCDQAMIEEWVFHVPHVGMFLSVVVHRGLCLLGSSFDPSTL
          ..Q.M.AQLLSEMKFQD...F.G.QCLDQ.CDQAM.EEWVFHVP.VG.FLSVV.H..LCLLG.SFD..TL
Retrocopy AVQVMAAQLLSEMKFQDAHQFLGLQCLDQICDQAMMEEWVFHVPWVGVFLSVVIHKCLCLLGPSFDHFTL

Parental  VPECLADQGGRFESILDVLSVIYLSSHLAPEHRQRWRLLFSTQLHGQSFSQLCSHITSQGPSLLVLEDRD
          VPEC..DQG..FESI.DVLSVIYLSSHLA.EHRQ.W.LLFSTQ.HGQSFSQLC...T.QGPSL.VL.DR.
Retrocopy VPECHMDQGRPFESIPDVLSVIYLSSHLAVEHRQLWCLLFSTQFHGQSFSQLCCLVTNQGPSLIVLKDRN

Parental  GYVFGGFASCSWEVKPQFQGDNRCFLFSIA-PRMATHLHT-GYNNHFMYLNYGQQTMPNGLGMGGQHHYF
          GYVFGGFASCSWEVKPQFQGDN.CFLFSIA.PRMATHLHT.GYNNHFMYLNY.QQ..PNGLGMGGQHHYF
Retrocopy GYVFGGFASCSWEVKPQFQGDNKCFLFSIA>PRMATHLHT<GYNNHFMYLNYRQQSIPNGLGMGGQHHYF

Parental  GLWVAADFGKGHSKAKPACTTYNSPQLSAQEDFLFDKMEVWGLGNL--LEEYEGKNKKSVLDSNPEARSL
          GLWV.ADFGKGHSK.KPACTTYNS.QLSAQEDFLFD.MEVWGLG....LE.Y..KN.KS.LDSNP...SL
Retrocopy GLWVVADFGKGHSKPKPACTTYNSTQLSAQEDFLFDNMEVWGLGDIYFLEIYQDKNRKSILDSNPDVHSL

Parental  LEISGRARHSEGLREVPRDED
          LEIS....HSEGL.EVP.DED
Retrocopy LEISRWI*HSEGLQEVPKDED

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	9.16 RPM
SRP007412_cerebellum	0.00 RPM	6.56 RPM
SRP007412_heart	0.00 RPM	11.39 RPM
SRP007412_kidney	0.00 RPM	7.85 RPM
SRP007412_liver	0.00 RPM	5.19 RPM
SRP007412_testis	0.00 RPM	8.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_343 was not detected

EST

No EST(s) were mapped for retro_mmus_343 retrocopy.

TSS

No TSS is located nearby retro_mmus_343 retrocopy 5' end.

Lab

retro_mmus_343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_343 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000034105	1 retrocopy	retro_mmus_343 ,
Sarcophilus harrisii	ENSSHAG00000001945	1 retrocopy	retro_shar_3,