RetrogeneDB ID: retro_ogar_883

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873530.1:7508301..7508987(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MITD1
• Ensembl ID: ENSOGAG00000002240
• Aliases: None
• Description: MIT, microtubule interacting and transport, domain containing 1 [Source:HGNC Symbol;Acc:25207]

Sequence

>retro_ogar_883
ATACTATAGCGGGCGGTGAAACTAGATTCGAGTACAGGTATCCGCAGGCTCTGGTATGTTACCAAGAAATGATTGATCTG
CTCCTACAAATTATAAAAAGCACCAAAGATTGTACTAAGGAGTCTAATCTCAGAGATAAAATTTCCAGCTACATGGAGAG
AGCAGAAAACATAAAGAAATACTTGGCTCAAGAAAAAGAAAATGGAAAATATCACAAGCAAATTAAAATAGAAGAGAATG
CAACAGGTTTCAGTTATGAATCACTTTTTCAAGAATACCTTAATGAGACAGACGTTTGGATAGAAGATCCTTATATTAGA
CAAATTCATCAGCTGCATAACTTTCTTTGATTTTGTGAGATACTTATTAAGAGATCATTTAAAGTAAAAATCATTCACCT
TCTCACCTCTCTGGATAAAGGCAGTGGGAAAGAATAGCAAATTAGGGGCCTGGAAGAAATAAAAGAGTCACTCAAGAATC
ATCAAGTGCTGTTGGAAGCAGACTATTCTCCCTCAATACATAACCAAGAAATTAGGTTCAACAATGGATGGATAATTAAG
ATTGGAAGAGGACTTGATTATTTTAAGAGAACACAGGGTCATTTTTCCTTTGAATATTTGGATTTTGATTTACAACCACG
TCATGAAACAATAGTGGACATTTTTCATAACAGACACACAAAAAAA

Alignment

ORF - retro_ogar_883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 92.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLQRAVKLDA-EYKYPQALICYQEGIDLLLQVMKGTKDCTKKSNLRDKISGYMERAENIKKYLAQEKEDG
          .L.RAVKLD..EY.YPQAL.CYQE.IDLLLQ..K.TKDCTK.SNLRDKIS.YMERAENIKKYLAQEKE.G
Retrocopy IL*RAVKLDS<EYRYPQALVCYQEMIDLLLQIIKSTKDCTKESNLRDKISSYMERAENIKKYLAQEKENG

Parental  KYHKQIKIEENATGFSYESLFQEYLNETVTEVWIEDPYIRQIHQLHNFLRFCEILIKRSSKVKIIHLLTS
          KYHKQIKIEENATGFSYESLFQEYLNET...VWIEDPYIRQIHQLHNFL.FCEILIKRS.KVKIIHLLTS
Retrocopy KYHKQIKIEENATGFSYESLFQEYLNET--DVWIEDPYIRQIHQLHNFL*FCEILIKRSFKVKIIHLLTS

Parental  LDKGNGKEQQIRGLEEIKESLKNHEVLLEVEYSPSIHDREIRFNNGWIIKIGRGLDYFKRTQGRFSLGYF
          LDKG.GKE.QIRGLEEIKESLKNH.VLLE..YSPSIH..EIRFNNGWIIKIGRGLDYFKRTQG.FS..Y.
Retrocopy LDKGSGKE*QIRGLEEIKESLKNHQVLLEADYSPSIHNQEIRFNNGWIIKIGRGLDYFKRTQGHFSFEYL

Parental  DFDLRPCHETTVDIFHNRHTKK
          DFDL.P.HET.VDIFHNRHTKK
Retrocopy DFDLQPRHETIVDIFHNRHTKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_883 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000010970	1 retrocopy	retro_cpor_196,
Otolemur garnettii	ENSOGAG00000002240	1 retrocopy	retro_ogar_883 ,
Sorex araneus	ENSSARG00000000765	1 retrocopy	retro_sara_766,