RetrogeneDB ID: retro_ogar_2321

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873611.1:526744..527408(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA1L2
• Ensembl ID: ENSOGAG00000029707
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]

Sequence

>retro_ogar_2321
ATTTGCTTTTGTGATCGTGATTCTATGGATAAGATGTCATTCAGAAATACCATACTGTGAATGGCCACAGTAAGTGTGAA
GTAAGGTAAGCCCTGTAGAAGAAAGAGATGGCTAGTGCTTCATTCAGCCAAAGAGGTCAGAGTGGTTCTGGGAACCTTGG
TGGCGGTCGTGGAGGTGGTCTTGGTGGAAATGACTTTAACCATGAAAGAAACTTCAGTGGTTGTGGTGGCTTTGGTGGAG
CCATAGTAGTGGTGGATATGGTGGCAATGGATTTGGTAATGATGATGATTATGGAGGAGATAGCCCTGCTTACTCTGCAG
GAAGCAGAGGCTACAGAAGTAGTAGACAGGGTTGTGGGAACCAGGCCAGTGGCTATGGTGGGAGTGGCAGCTATGACAGC
CCTAACAACAGAGGAGGTGGAGGTGGCTTTGGTGGTGGTAGTGGAAGCAATTTTGAAGATAGTGGAAGCTACAATGAATG
ATTTAGGCAATTACAGCAATCAGTCTAGTCTTCAAATTTTGGACCCACATAAAGGGAGGACATTTTGGAGGCAGAAGCTC
TGGCCTCTATTGGTGGTGGCAGCCAATACTTTGCCAAATCAGAAAACCAAGGTGGCTATGGTGGTTCCAATAGCAGCATT
AGCTATGGCAGTGGCATAAGGTTT

Alignment

ORF - retro_ogar_2321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.53 %
• Parental protein coverage: 60.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VTFDDHDSVDKI-VIQKYHTVNGHN-CEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGR
          ..F.D.DS.DK..VIQKYHTVNGH..CEVR.AL.K.EMASAS.SQRG.SGS....G..GGG.GG....G.
Retrocopy ICFCDRDSMDKM<VIQKYHTVNGHSKCEVR*AL*KKEMASASFSQRGQSGS----GNLGGGRGG----GL

Parental  GGN-FSGRGGFGGSRG-GGG-YGGSGDGYNGFGNDGGYGGGGPGYTGGSRGYGSGGQGYGNQGSGYGGSG
          GGN.F.....F.G..G.GG......G.G.NGFGND..YGG..P.Y..GSRGY.S..QG.GNQ.SGYGGSG
Retrocopy GGNDFNHERNFSGCGGFGGA<HSSGGYGGNGFGNDDDYGGDSPAYSAGSRGYRSSRQGCGNQASGYGGSG

Parental  SYDSYNNGGGGGGFGGGSGSNFGGGGSYNDFGNYNNQS---SNFGPM-KG-GNFGGRSSGPY-GGGGQYF
          SYDS.NN.GGGGGFGGGSGSNF...GSYN.......QS...SNFGP..KG.G.FGGRSSG.Y.GGG.QYF
Retrocopy SYDSPNNRGGGGGFGGGSGSNFEDSGSYNE*FRQLQQSV*SSNFGPT>KG>GHFGGRSSGLY>GGGSQYF

Parental  AKPRNQGGYGGSSSSSSYGSGRRF
          AK..NQGGYGGS.SS.SYGSG.RF
Retrocopy AKSENQGGYGGSNSSISYGSGIRF

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_2321 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 14 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000717	3 retrocopies	retro_amel_1726, retro_amel_547, retro_amel_925,
Canis familiaris	ENSCAFG00000006580	16 retrocopies	retro_cfam_1080, retro_cfam_1081, retro_cfam_1170, retro_cfam_1323, retro_cfam_1616, retro_cfam_1844, retro_cfam_2017, retro_cfam_2128, retro_cfam_360, retro_cfam_564, retro_cfam_702, retro_cfam_803, retro_cfam_839, retro_cfam_855, retro_cfam_892, retro_cfam_937,
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Macaca mulatta	ENSMMUG00000012989	5 retrocopies	retro_mmul_1031, retro_mmul_1427, retro_mmul_1726, retro_mmul_187, retro_mmul_1871,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Otolemur garnettii	ENSOGAG00000015353	3 retrocopies	retro_ogar_1384, retro_ogar_3077, retro_ogar_3189,
Otolemur garnettii	ENSOGAG00000025948	3 retrocopies	retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321 ,
Otolemur garnettii	ENSOGAG00000030251	2 retrocopies	retro_ogar_3509, retro_ogar_385,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,