RetrogeneDB ID: retro_ogar_882

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873530.1:6970419..6971127(+)
• Located in intron of: ENSOGAG00000005900

Retrocopy information

• Ensembl ID: ENSOGAG00000025577
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC39A9
• Ensembl ID: ENSOGAG00000015110
• Aliases: None
• Description: solute carrier family 39, member 9 [Source:HGNC Symbol;Acc:20182]

Sequence

>retro_ogar_882
GGAAAGCATCATCAAGCAAGTGAAACACAGAACGTGACTGCCTCAGACAAAGCGGCAGAAATATCAGCTGTCCATGAACA
TGAGCACAGCCACAGACACACACACCTGCACCCCTGCATTGGGGTTTCCCTGGTACTGGGCTTCGTGTTCATGTTGCAGA
TCGGCAGTTCCCACGTGCGTTCTGCTGAGGATCCAGAAGCAGCAAGATGGAGCAGTTCCCAAATCACCCCCACACTGGGG
CTGGCTGTCCACGCTGCGGCTGATGGTGTTGCCTTGGGAGCAGCAGCTTCTACTTCACAGACTAGTGTGCAGTTAATTGT
GTTTGTGGCAATAATGCTACATAAGGCACCAGCTGCTTTGGGACTGGGTTCCTTCTTAATGCATGCCGGCCTAGAGCGGA
ATCGAATCAGAAAGCACTTGCTGGTCTTGGTGCTGGCAGCACCAGTTATATCCATGATGACATACTTGGGACTAAGTAAG
AGCAGTAAAGAAGCCCTCTCAGGGGTGAATGCCACTGGAGTGGCCATGCTCTTCTCTGCTGGGACATTTCTTTATGTTGT
TACAGTACACGTCCTCCCCAAGGTGGGAGGAATGGGGCACAGCCACCAGCCTGACACCACTGGAGGGAGAGGCCTCAGCC
GCCTGGAGGAGGCGGCTCTGGTTCTGGGTTGCCTCATCCCACTCATCCTGTCGCTGGGAAACCAGTAT

Alignment

ORF - retro_ogar_882 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKHHQASETQNVIASDKAAEIPVVHEHEHSHNHTELHAYIGVSLVLGFVFMLLVDQIGNSHVHSADDPEA
          GKHHQASETQNV.ASDKAAEI..VHEHEHSH.HT.LH..IGVSLVLGFVFML...QIG.SHV.SA.DPEA
Retrocopy GKHHQASETQNVTASDKAAEISAVHEHEHSHRHTHLHPCIGVSLVLGFVFML---QIGSSHVRSAEDPEA

Parental  ARSSSSKITTTLGLVVHAAADGVALGAAASTSQTSVQLIVFVAIMLHKAPAAFGLVSFLMHAGLERNRIR
          AR.SSS.IT.TLGL.VHAAADGVALGAAASTSQTSVQLIVFVAIMLHKAPAA.GL.SFLMHAGLERNRIR
Retrocopy ARWSSSQITPTLGLAVHAAADGVALGAAASTSQTSVQLIVFVAIMLHKAPAALGLGSFLMHAGLERNRIR

Parental  KHLLVFALAAPVMSMATYLGLSKSSKEALSEVNATGVAMLFSAGTFLYVATVHVLPEVGGMGHSHKPDTT
          KHLLV..LAAPV.SM.TYLGLSKSSKEALS.VNATGVAMLFSAGTFLYV.TVHVLP.VGGMGHSH.PDTT
Retrocopy KHLLVLVLAAPVISMMTYLGLSKSSKEALSGVNATGVAMLFSAGTFLYVVTVHVLPKVGGMGHSHQPDTT

Parental  GGRGLSRLEVAALVLGCLIPLILSVGHQH
          GGRGLSRLE.AALVLGCLIPLILS.G.Q.
Retrocopy GGRGLSRLEEAALVLGCLIPLILSLGNQY

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_882 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000015110	1 retrocopy	retro_ogar_882 ,