RetrogeneDB ID: retro_ogar_1400

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873545.1:40826..41704(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAE1
• Ensembl ID: ENSOGAG00000014649
• Aliases: None
• Description: RAE1 RNA export 1 homolog (S. pombe) [Source:HGNC Symbol;Acc:9828]

Sequence

>retro_ogar_1400
AGGACAGTGGGCAAACCATTCCAAAAGCCCAGCAGATGCACACAGGGCCTGTGCTAGAGTGACGATGGGAGCAAAGTACT
TACAGCATCATGTGATAAAACTGCTAAATGTGGGTTCTCAACAGTAATCAAGCGATATAGATTGCACAGCATGATGCTCC
TGTTAAAACCATACATTGGATCAAAGCTCCAAACTACAGCTGTGCGATGACTGGGAGCTGGGATAGGACTTTAAAGTTTG
GGGATACTCGGTCATCAAATCCTATGATGGTTTTGCCACTCCCTGAAAGCTGTTATTGTGCTGATGTGATATACCCTATG
GCCGTGATGGCAACTGCAGAGAGGGCCCTAATTGTATACCAATTAGACAATCAAGGTTCTGAGTTCAGGAGGATAGAATC
TCCACTGAAACATCAGCATTGAAGCGTAGCTGTTTTTAAAGACAAACAGAACAAGCCAACTGGTTTTGCCCTGGGAAGTA
TTGAGGGAAGAGTTGGTATTCACTACATCAACCCCCCAAATCCTGCCAAAGATAACTTTACCGTTAAATGTCATCGATCT
AATGGAACCAACACTTCAGCTCCTCAAGACATCTATGTGGTAAATGGAACCCCATTCCATCCTGTTCGTGGCACCCTTGC
GACTGTGGGATCTGCTGGTAGATTCAGCTTCTGGAACAAAGATGCCAGAACAAAACTAAAAACTCCAGAACAGGTGGGTC
AGCCAGTATCAGCTTTTTGCTTCAATCACAATGGAAACATGTATGCATATGATTCCAGCTAAGACTGGTCAAAGGGATAT
GAGTTTTACAATCCCCAAAAGAAAAATTACATTTTCCTGCATAATGCAGCAGAAGAGCTAAAACTGAGGAATAAGAAG

Alignment

ORF - retro_ogar_1400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 79.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QTIPKAQQMHTGPVLDVCWSDDGSKVFTASCDKTAK-MWDLNSNQAIQIAQHDAPVKTIHWIKAPNYSCV
          .T..K..Q.........C.SDDGSKV.TASCDKTAK.MW.LNSNQAI.IAQHDAPVKTIHWIKAPNYSC.
Retrocopy RTVGKPFQKPSRCTQGLC*SDDGSKVLTASCDKTAK<MWVLNSNQAI*IAQHDAPVKTIHWIKAPNYSCA

Parental  MTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQPSEFRRIESPLKHQ
          MTGSWD.TLKF.DTRSSNPMMVL.LPE.CYCADVIYPMAV.ATAER.LIVYQL.NQ.SEFRRIESPLKHQ
Retrocopy MTGSWDRTLKFGDTRSSNPMMVLPLPESCYCADVIYPMAVMATAERALIVYQLDNQGSEFRRIESPLKHQ

Parental  HRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPV
          H..VA.FKDKQNKPTGFALGSIEGRV.IHYINPPNPAKDNFT.KCHRSNGTNTSAPQDIY.VNG..FHPV
Retrocopy H*SVAVFKDKQNKPTGFALGSIEGRVGIHYINPPNPAKDNFTVKCHRSNGTNTSAPQDIYVVNGTPFHPV

Parental  HGTLATVGSDGRFSFWDKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSYDWSKGHEFYNPQKKNYIF
          .GTLATVGS.GRFSFW.KDARTKLKT.EQ..QP.SA.CFNHNGN..AY.SS.DWSKG.EFYNPQKKNYIF
Retrocopy RGTLATVGSAGRFSFWNKDARTKLKTPEQVGQPVSAFCFNHNGNMYAYDSS*DWSKGYEFYNPQKKNYIF

Parental  LRNAAEELKPRNKK
          L.NAAEELK.RNKK
Retrocopy LHNAAEELKLRNKK

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_1400 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
Oryctolagus cuniculus	ENSOCUG00000001585	2 retrocopies	retro_ocun_1819, retro_ocun_646,
Otolemur garnettii	ENSOGAG00000014649	2 retrocopies	retro_ogar_1400 , retro_ogar_2829,
Ochotona princeps	ENSOPRG00000000228	1 retrocopy	retro_opri_1149,
Sarcophilus harrisii	ENSSHAG00000000550	1 retrocopy	retro_shar_812,
Sarcophilus harrisii	ENSSHAG00000002438	1 retrocopy	retro_shar_811,