RetrogeneDB ID: retro_ogar_3305

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873772.1:160573..161215(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000024494
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CTDSPL
• Ensembl ID: ENSOGAG00000004624
• Aliases: None
• Description: CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like [Source:HGNC Symbol;Acc:16890]

Sequence

>retro_ogar_3305
AAGAAAGCTTCACAATGCAACATCAGCTTAAAGAAGCAGAGGAGCCGCAGCATCCTCAGCTTCTTCTTCTGCTGCTTGGG
TGATTATAATGTGGAGGCCGCTAGGCCCAGCAGCCCCAGTGTGCTTTCGCCACTGGTGGAGGAGAATGTTGGGCTCCGGA
AGGGTGACCAGAGGCAGGTCATTCCCATACCAAGTACACCAGCTAAATACATCCTTCCTGAGGTGACAGGGCTTGACTAT
GGAAAGAAATGTGTGGTCATTGATTTAGATGAAACACGGGTGCACAGCTCATTTAAGCCTATTAGTAATGCTGATTTTAT
TGTTCTGGTTGAAATCGATGGAACTATACATCAGGTATATGTGCTGAAGTGGCCACATGTGGATGAGTTCCTCCAGAGGA
TGGGGCAGCTCTTTGAGTGTGTGTTCTTTACTGCCAGCTTGGTAAAGTATGCAGACCCCGTGGCTGACCTCCAAGACCGC
TGGGGTGTGTTCCAAGCCCGGCTTCTCAGAGAGTCTTGTGTTTTTCATCGTGGGAACTACGTGAAGGACCCGAGTCACCT
TGGACGGGAGCTGAGCAAAGTAATCATTGTTGACAATTCTCCTGCCTCATACATCTTCCATCCTGAGAATGCAGTCCTGG
TT

Alignment

ORF - retro_ogar_3305 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.32 %
• Parental protein coverage: 77.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKPSQCNISLKKQRSRSILSSFFCCFRDYNVEAPPPSSPNVLPPLVEENGGLQKGDQRQVIPIPSPPAKY
          .K.SQCNISLKKQRSRSILS.FFCC..DYNVEA..PSSP.VL.PLVEEN.GL.KGDQRQVIPIPS.PAKY
Retrocopy KKASQCNISLKKQRSRSILSFFFCCLGDYNVEAARPSSPSVLSPLVEENVGLRKGDQRQVIPIPSTPAKY

Parental  LLPEVTVLDYGKKCVVIDLDETLVHSSFKPISNADFIVPVEIDGTIHQVYVLKRPHVDEFLQRMGQLFEC
          .LPEVT.LDYGKKCVVIDLDET.VHSSFKPISNADFIV.VEIDGTIHQVYVLK.PHVDEFLQRMGQLFEC
Retrocopy ILPEVTGLDYGKKCVVIDLDETRVHSSFKPISNADFIVLVEIDGTIHQVYVLKWPHVDEFLQRMGQLFEC

Parental  VLFTASLAKYADPVADLLDRWGVFRARLFRESCVFHRGNYVKDLSRLGRELSKVIIVDNSPASYIFHPEN
          V.FTASL.KYADPVADL.DRWGVF.ARL.RESCVFHRGNYVKD.S.LGRELSKVIIVDNSPASYIFHPEN
Retrocopy VFFTASLVKYADPVADLQDRWGVFQARLLRESCVFHRGNYVKDPSHLGRELSKVIIVDNSPASYIFHPEN

Parental  AVPV
          AV.V
Retrocopy AVLV

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_3305 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	ENSOGAG00000004624	1 retrocopy	retro_ogar_3305 ,