RetrogeneDB ID: retro_ogar_985

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873532.1:21441482..21442127(-)
• Located in intron of: ENSOGAG00000002780

Retrocopy information

• Ensembl ID: ENSOGAG00000024401
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSOGAG00000009456
• Aliases: None
• Description: RAB5C, member RAS oncogene family [Source:HGNC Symbol;Acc:9785]

Sequence

>retro_ogar_985
ATGGTGGGTCGGGGAGGCACAGCACGACCCAATGGGCCAGCTGCTGGGAACAAGATCTGTCAGTTTAAGCTGGTTCTGCT
GGGGGAGTCTGCAGTGGGCAAGTCCAGCCTCGTCCTCCGCTTTGTCAAGGTACAATTCCACGAGTACCAGGAAAGCACAA
TTGGAGCGGCCTTCCTCACACAGACTGTCTGCTTGGACGACACAACGGTCAAGTTTGAGATCTGGGACACAGCTGGACAG
GAGCGGTATCACAGCCTGGCCCCCATGTACTATCGGGGGGCCCAAGCTGCCATCGTGGTCTATGACATCACCAATACAGA
TACATTTGCACGGGCCAAGAACTGGGTGAAGAAGTTACAAAGGCAGGCCAGCCCCAACATCGTCATTGCACTTGCGGGTA
ACAAGGCGGATCTGGCCAGCAAGAGAGCCGTGGAATTCCAGGAAGCACAAGCCTATGCAGACAACAGTTTGCTGTTCATG
GAGACATCGGCAAAGACTGCAATGAATGTGAATGAAATTTTCATGGCAATAGCTAAGAAGCTTCCCAAGAATGAGCCCCA
GAATGCAGCTGGTGCTCCAGGCCGAAACCAAGGTGTGGACCTCCAGGAGAATAACCCAGCCAGCCGGAGCCAGTGCTGCA
GCAAC

Alignment

ORF - retro_ogar_985 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGRGGTARPNGPAAGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTV
          M.GRGGTARPNGPAAGNKICQFKLVLLGESAVGKSSLVLRFVK.QFHEYQESTIGAAFLTQTVCLDDTTV
Retrocopy MVGRGGTARPNGPAAGNKICQFKLVLLGESAVGKSSLVLRFVKVQFHEYQESTIGAAFLTQTVCLDDTTV

Parental  KFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLAS
          KFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVK.LQRQASPNIVIALAGNKADLAS
Retrocopy KFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKKLQRQASPNIVIALAGNKADLAS

Parental  KRAVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKLPKNEPQNAAGAPGRNRGVDLQENNPASR
          KRAVEFQEAQAYA.DNSLLFMETSAKTAMNVNEIFMAIAKKLPKNEPQNAAGAPGRN.GVDLQENNPASR
Retrocopy KRAVEFQEAQAYA-DNSLLFMETSAKTAMNVNEIFMAIAKKLPKNEPQNAAGAPGRNQGVDLQENNPASR

Parental  SQCCSN
          SQCCSN
Retrocopy SQCCSN

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_985 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006003	1 retrocopy	retro_amel_543,
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Otolemur garnettii	ENSOGAG00000009456	2 retrocopies	retro_ogar_2175, retro_ogar_985 ,
Otolemur garnettii	ENSOGAG00000015779	1 retrocopy	retro_ogar_2851,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,