RetrogeneDB ID: retro_ogar_349

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:42623967..42624578(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000000741
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KIAA1704
• Ensembl ID: ENSOGAG00000012513
• Aliases: None
• Description: KIAA1704 [Source:HGNC Symbol;Acc:20298]

Sequence

>retro_ogar_349
CAGGAAACAGATAGCAGTGAAGATGAGGACATCAATGGACCAATGCCTGCAAAAGGACCAGTTAACTGCTGTGTTAACAA
CAGAGTTTGAAAAAAGAGCCCAGAGAATGAAAGAAAAACTTAGATGATGATTCTTCTAAACCAATTACAAGAGAGTTATG
GATGACAGAGCTTCCTCCAGAAATGAAAGACTTTGGTCTTGGGCCAACAACTTTCAAGAGAGAGCCAATGACAAATCCGG
AGGTCGATCAATCTGGACAGATACTCCAGCTGAAAGGGAAAGGAAAGCTAAGGAAACACAAGAAGCAAGGAAGTCATTCA
ATAAGAAGGATGAAGAACATATATTGTCAGGAAGAGATAAGAGACTGGCTGAGCAGGTATTCTCAAATAATGAATCAAAA
AGATCAGAATCTCTTATGGAGAGATCTCTCCATCATAAGAAATTAAAGAGTAAGGCTGATGAAGATAAAAACAAGCCTCA
AGAGAATACCACTTGAATGTGATAAGGATCTCAAGGTTAATCAGTTTGATGAAACTCAGAAAAAAGCCCTAATAAAGAAA
TCTAAATCACTAAACAGTAGATTTTCACATGGCAAAAGCAATATGTTTTTA

Alignment

ORF - retro_ogar_349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.81 %
• Parental protein coverage: 59.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KDTDSSEDEDIIGPMPAKGPVNYCV-TTEF-EKRAQRMKEKLTKGNDDSSKPIIRESWMTELPPEMKDFG
          ..TDSSEDEDI.GPMPAKGPVN.CV.TTEF..K.....K..L....DDSSKPI.RE.WMTELPPEMKDFG
Retrocopy QETDSSEDEDINGPMPAKGPVNCCV>TTEF>KKEPRE*KKNL---DDDSSKPITRELWMTELPPEMKDFG

Parental  LGPRTFKR-RADDKSGDRSIWTDTPADRERKAKEAQEARKSFNKKDEEHILSGRDKRLAEQVSSYNESKR
          LGP.TFKR.RA.DKSG.RSIWTDTPA.RERKAKE.QEARKSFNKKDEEHILSGRDKRLAEQV.S.NESKR
Retrocopy LGPTTFKR<RANDKSGGRSIWTDTPAERERKAKETQEARKSFNKKDEEHILSGRDKRLAEQVFSNNESKR

Parental  SESLMDIH-HKKLKSKAAEDKNKPQE-RIPFDRDKDLKVNRFDEAQKKALIKKSRELNTRFSHGKSNMFL
          SESLM....H.K.....A.........RIP...DKDLKVN.FDE.QKKALIKKS..LN.RFSHGKSNMFL
Retrocopy SESLMERSLHHKKLKSKADEDKNKPQ>RIPLECDKDLKVNQFDETQKKALIKKSKSLNSRFSHGKSNMFL

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_349 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019204	1 retrocopy	retro_cjac_513,
Otolemur garnettii	ENSOGAG00000012513	1 retrocopy	retro_ogar_349 ,