RetrogeneDB ID: retro_ogar_3090

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873712.1:1217944..1218679(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000010115
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CALCOCO2
• Ensembl ID: ENSOGAG00000011709
• Aliases: None
• Description: calcium binding and coiled-coil domain 2 [Source:HGNC Symbol;Acc:29912]

Sequence

>retro_ogar_3090
ACTCAGGGAGAAGTGGAAGAGATTGAAGAGCAAAATAAGGAGCTTTGCAAAGAAAACCAGGAGCTGAAGGACAGCTGTGT
CAGCCTCCAGAAGCAGAACTCAGACATGCAGGCTGAGCTCCAAAGGAAGCAGGAAGAGCTAGAAACCCTCCAGAGCATCA
ATAAGAAGTTGGAACAGAAAGTGAAAGACCAGAAGGACTGTTGGGAGACAGAACTGCTTCAGCTGAAAGAACAAAACCAG
AAAGTGTCCTTAGAAAATGAAAAGATGGGAATCAGAGTGCATCAGCTTCAGGTCCAGCTGTCAACTCAAGAGAAGGAAAT
GGAGCAGCTTGTTCAGAGAGCTCAAGATAAGACAGAACAGTTAGAGCATCTGAAAAAGGAAAATGGCCAACTCTTTCTCA
CTCTAACTGAACAGAGGGAGCACCAGAAGAAGCTCGAGCAGACAGTGGAGGAGATGAAGCAAAAGGAAACCACTGCCCTG
AAGAAGCAACAGGAGTTAATGGATGAGAACTTTGACCTGTCAAGAAGACTGAGTGAGAACAAGATTATATACGATGCTCT
GCAGAGAGATAAAGAGAGACTAGAAAAAGAAAATGATCTTTTGAAGAAGGAGAACAACAGATTGCTCTGTTACATGGGTC
TGGATTTTGACTCTTTGCCGCATCACGTGCCTACTTCAGAGCAGGGAGGTGCAGGACAAAATGCAGGACTTGCCCATGGA
AACCCATATTCTGGT

Alignment

ORF - retro_ogar_3090 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.96 %
• Parental protein coverage: 63.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSGEVEEIEEQNKELCKENQELKDSCVSLQKQNSDMQAELQRKQEELETLQSINKKLEQKVKDQKDCWET
          T.GEVEEIEEQNKELCKENQELKDSCVSLQKQNSDMQAELQRKQEELETLQSINKKLEQKVKDQKDCWET
Retrocopy TQGEVEEIEEQNKELCKENQELKDSCVSLQKQNSDMQAELQRKQEELETLQSINKKLEQKVKDQKDCWET

Parental  ELLQLKEQNQKVSLENEKMGIRVDQLQAQLSTQEKEMEQLVQRAQDKTEQLERLKKENGQLFLTLTEQRE
          ELLQLKEQNQKVSLENEKMGIRV.QLQ.QLSTQEKEMEQLVQRAQDKTEQLE.LKKENGQLFLTLTEQRE
Retrocopy ELLQLKEQNQKVSLENEKMGIRVHQLQVQLSTQEKEMEQLVQRAQDKTEQLEHLKKENGQLFLTLTEQRE

Parental  HQKKLEQTVEEMKQKETTALKKQQELMDENFDLSRRLSENKIIYDALQRDKERLEKENDLLKKENNRLLC
          HQKKLEQTVEEMKQKETTALKKQQELMDENFDLSRRLSENKIIYDALQRDKERLEKENDLLKKENNRLLC
Retrocopy HQKKLEQTVEEMKQKETTALKKQQELMDENFDLSRRLSENKIIYDALQRDKERLEKENDLLKKENNRLLC

Parental  YMGLDFDSLPHHVPTSEQGGAGQNAGLAYGNPYSG
          YMGLDFDSLPHHVPTSEQGGAGQNAGLA.GNPYSG
Retrocopy YMGLDFDSLPHHVPTSEQGGAGQNAGLAHGNPYSG

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_3090 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000006056	3 retrocopies	retro_mmus_1016, retro_mmus_1108, retro_mmus_2097,
Otolemur garnettii	ENSOGAG00000000427	1 retrocopy	retro_ogar_3134,
Otolemur garnettii	ENSOGAG00000011709	1 retrocopy	retro_ogar_3090 ,
Rattus norvegicus	ENSRNOG00000031074	1 retrocopy	retro_rnor_1194,
Ictidomys tridecemlineatus	ENSSTOG00000013395	1 retrocopy	retro_itri_1120,