RetrogeneDB ID: retro_ogar_2949

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873687.1:3611797..3612558(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000025625
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTPLB
• Ensembl ID: ENSOGAG00000014549
• Aliases: None
• Description: protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b [Source:HGNC Symbol;Acc:9640]

Sequence

>retro_ogar_2949
ATGGCAGCAGCGGCAGCGACTGCGGCAACGAAGGGGAATGGGGTTGGAGGTGGCCGGGCTGGGGCTGGCAAAGCCAGCAT
TGCACGGAAGAAGAAGGGTCTGGGGCCTCTTGCCATGGTGTACCTGGTCATCTACAATGTGGTGATGACTGTGGGGTGGC
TGGTGATAGCAGTTGGTCTGGTCAGAGCATACCTGGCTAAGGGTAGCTACCATAGTCTTTATTATTCATTGAAAAGCCTT
TGAAATTCTTCCAAACTGGAGCCTTCTTGGAGATTTTGCACTGTGCTATAGGAATTGTTCCATCCTCTGTTGTCCTGACT
TCTTTCCAGGTGATGTCAAGAGTTTTTTCTAATATGGGCAGTAACATATAGCGTCAAAGAGGTACAGTGTGAAGACAGTG
TCCTCCTGTTTGTCATTGCCTGGACAATCGTGGAGATTATCCATTACTCCTTTTATACTTTCAGTCTGTTAAAGTATCTG
CCTTACCTCTTCAAGTGGACCAGATACACACTTTTCATTGTGTTGTACCCAATGGGAGTGTCAGGAGAGCTGCTTACAAT
GTATGCAGCCCTGCCCTTTGTCAGACAGGCCGCCTGTACTCCATCAGTTTACCCAACAAGTACAATTTCTCCTTCCACTA
CTACCTGTTCCCAGTCCTAATAATGATCTGTTACATTTCTATTTTTCCCCAGTTGTACTTCCACATGATACATCAGAGAA
GAAAGGTCCTTTCTCATACCGAAGAACACAAGAAATTTGAA

Alignment

ORF - retro_ogar_2949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAAAATAATKGNGVGGGRAGAGEASGARKKKGPGPLATAYLVIYNVVMTAGWLVIAVGLVRAYLAKGSY
          MAAAAATAATKGNGVGGGRAGAG.AS.ARKKKG.GPLA..YLVIYNVVMT.GWLVIAVGLVRAYLAKGSY
Retrocopy MAAAAATAATKGNGVGGGRAGAGKASIARKKKGLGPLAMVYLVIYNVVMTVGWLVIAVGLVRAYLAKGSY

Parental  HSLYYS-IEKPLKFFQTGALLEILHCAIGIVPSSVVLTSFQVMSRVF-LIWAVTHSVKEVQSEDSVLLFV
          HSLYYS.IEKPLKFFQTGA.LEILHCAIGIVPSSVVLTSFQVMSRVF.LIWAVT.SVKEVQ.EDSVLLFV
Retrocopy HSLYYS<IEKPLKFFQTGAFLEILHCAIGIVPSSVVLTSFQVMSRVF>LIWAVTYSVKEVQCEDSVLLFV

Parental  IAWTITEIIRYSFYTFSLLNHLPYLIKWARYTLFIVLYPMGVSGELLTMYAALPFVRQAG-LYSISLPNK
          IAWTI.EII.YSFYTFSLL..LPYL.KW.RYTLFIVLYPMGVSGELLTMYAALPFVRQA..LYSISLPNK
Retrocopy IAWTIVEIIHYSFYTFSLLKYLPYLFKWTRYTLFIVLYPMGVSGELLTMYAALPFVRQAA<LYSISLPNK

Parental  YNFSFDYYAFLILIMISYIPIFPQLYFHMIHQRRKVLSHTEEHKKFE
          YNFSF.YY.F..LIMI.YI.IFPQLYFHMIHQRRKVLSHTEEHKKFE
Retrocopy YNFSFHYYLFPVLIMICYISIFPQLYFHMIHQRRKVLSHTEEHKKFE

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_2949 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000035376	1 retrocopy	retro_mmus_1403,
Otolemur garnettii	ENSOGAG00000014549	1 retrocopy	retro_ogar_2949 ,