RetrogeneDB ID: retro_ogar_3150

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873730.1:2339974..2340614(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RTFDC1
• Ensembl ID: ENSOGAG00000004444
• Aliases: None
• Description: replication termination factor 2 domain containing 1 [Source:HGNC Symbol;Acc:15890]

Sequence

>retro_ogar_3150
ATGGGCTGCGATGGGAGAACAATCCCCAAGAGGCATGAACTGGTAAAGGGACCAAAGGAGGTTGAGAAGGTTGACAAAGA
TGCTGAATTAGTGGCCCAGTGGAACTCCTGTACTCTAAGTCAAGAAATATTAAGACGACCAATAGTTGCCTGTGAACTTG
GCAGACTTTATAACAAAGATGCTGTCGTTGAGTTTCTGTTGGACAAATCTGCTGAAAAGGCTCTGAGGAAGGAGCATCTC
ACATTAACAGCATTAAGAATGTGACTGAACTAAGGCTTTCTCATATTCCCGCCTGGGAAGGGGATAAAGGAAATACAAAA
GGCAATAAGCTCAAGGACCTCCTGCGGGTAATTTTCAATGGTCGCGCCATGCGCCTGGAGGTGAATGGCCAGCACAGGTT
CTGCTTCCTTCGGTACTGTGGGTGTGTGTTTTCTGAATGAGCCCTGAAAGAGATAAAAGCAGAAGTTTGTCACACATGTG
GAGCTACCTTCCAGGAGGATGACATCATTGTGCTCAATGGCACCAAGGAGGATGTGGAAGTGCTGAAGACAAGGTTGGAG
GACAGAGGCTGCGAGCAAAGCTGGAAAAGAAAACAAAGAAACCTAAAGCAGCAGAGTCTGTTTCAAAATCCGATGTTCTG

Alignment

ORF - retro_ogar_3150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.72 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGCDGGTIPKRHELVKGPKKVEKVDKDAELVAQWNYCTISQEILRRPIVACELGRLYNKDAVIEFLLDKS
          MGCDG.TIPKRHELVKGPK.VEKVDKDAELVAQWN.CT.SQEILRRPIVACELGRLYNKDAV.EFLLDKS
Retrocopy MGCDGRTIPKRHELVKGPKEVEKVDKDAELVAQWNSCTLSQEILRRPIVACELGRLYNKDAVVEFLLDKS

Parental  AEKALGK-AASHIKSIKNVTELRLSDNPAWEGDKGNTKGDKHDDLQRARFICPVVGLEMNGRHRFCFLRC
          AEKAL.K..ASHI.SIKNVTELRLS..PAWEGDKGNTKG.K..DL.R..F......LE.NG.HRFCFLR.
Retrocopy AEKALRK<GASHINSIKNVTELRLSHIPAWEGDKGNTKGNKLKDLLRVIFNGRAMRLEVNGQHRFCFLRY

Parental  CGCVFSERALKEIKAEVCHTCGAAFQEDDIVVLNGTKEDVEVLKTRMEER-RLRAKLEKKTKKPKAAESV
          CGCVFSE.ALKEIKAEVCHTCGA.FQEDDI.VLNGTKEDVEVLKTR.E.R.RLRAKLEKKTKKPKAAESV
Retrocopy CGCVFSE*ALKEIKAEVCHTCGATFQEDDIIVLNGTKEDVEVLKTRLEDR<RLRAKLEKKTKKPKAAESV

Parental  SKPDVL
          SK.DVL
Retrocopy SKSDVL

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_3150 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027390	1 retrocopy	retro_btau_1076,
Echinops telfairi	ENSETEG00000003143	1 retrocopy	retro_etel_2095,
Mus musculus	ENSMUSG00000027502	1 retrocopy	retro_mmus_339,
Ornithorhynchus anatinus	ENSOANG00000009249	1 retrocopy	retro_oana_124,
Otolemur garnettii	ENSOGAG00000004444	1 retrocopy	retro_ogar_3150 ,