RetrogeneDB ID: retro_ogar_1996

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873579.1:1761577..1761945(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CCDC169
• Ensembl ID: ENSOGAG00000010367
• Aliases: None
• Description: coiled-coil domain containing 169 [Source:HGNC Symbol;Acc:34361]

Sequence

>retro_ogar_1996
GATAGATGATCTTCTATTCGTGTCTATGAAGAAATGACAGTGGAATCCTTAAATACATTACTTAAACAGCTAGAAAAAGA
AAAAAGGAGACTTGAAAATCAAGTGAAAGACTACGCACTTAGGCTGGAACAAGAATCCAAGGCTTACCACAAGACCAACA
ATGAACACCATATATACCTAAATGAAATGTCTCGGGTCTCAAGCTCACATCAAGTGTCTAAACGGCAACAGATGGATCAA
GTGCCTAGAATGAAAGAGAATCTAGTGAAAATAGGAAGGTATAAGCCAGTTGACAGAAGATGGCAAATGGCAAGAAAGGA
CCCGTAAAAAAGATTACAAAATCAAACCATCTTCCAAAACTCAATCCA

Alignment

ORF - retro_ogar_1996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.32 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DRLSSIRVYEQMTVESLNTLLKQLEKEKRSLENQVKDYALRLEQESKAYHKTNNERRTYLNEMSQVSSSH
          DR.SSIRVYE.MTVESLNTLLKQLEKEKR.LENQVKDYALRLEQESKAYHKTNNE...YLNEMS.VSSSH
Retrocopy DR*SSIRVYEEMTVESLNTLLKQLEKEKRRLENQVKDYALRLEQESKAYHKTNNEHHIYLNEMSRVSSSH

Parental  QVSKRQQMDQLPRMKENLVKTGKYNPVD-QKMANGKKGPVKKITKSNHLPKLNP
          QVSKRQQMDQ.PRMKENLVK.G.Y.PVD.QKMANGKKGPVKKITKSNHLPKLNP
Retrocopy QVSKRQQMDQVPRMKENLVKIGRYKPVD<QKMANGKKGPVKKITKSNHLPKLNP

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_1996 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004615	1 retrocopy	retro_amel_120,
Equus caballus	ENSECAG00000011446	1 retrocopy	retro_ecab_111,
Felis catus	ENSFCAG00000008786	1 retrocopy	retro_fcat_39,
Otolemur garnettii	ENSOGAG00000010367	2 retrocopies	retro_ogar_1996 , retro_ogar_957,
Sus scrofa	ENSSSCG00000026564	1 retrocopy	retro_sscr_77,