RetrogeneDB ID: retro_pabe_3374

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8_random:2845223..2845754(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF2
• Ensembl ID: ENSPPYG00000000417
• Aliases: RNF2, RING1B
• Description: E3 ubiquitin-protein ligase RING2 [Source:RefSeq peptide;Acc:NP_001127433]

Sequence

>retro_pabe_3374
TTTGATGCACTCATCAGCAAAATTTACCCAGGTCATGATAAGTACGAAGCTCTTGGAGACAGAGTATTAGCCAGCATCCA
CAAGCACAGTAATCAGTGAGCACTCAGTCTCAGCTCTAAAGAAGGACTGAAGGTACCAGTCAGGAGCAGATTACAGTGAG
GCAAGAAACAATAGACTGAAAATGGTAGCAGAGCAGAAGAGAATGCTGATGGTTTGCATTGTAGTGGTGCATCCACACAG
AACAACAAGGAAACAGGCCATAGTCACAAATGGACGAAAACATCTGCCGACTCTGGGCTTGAGCTTGATATTGACAATGC
AACATTTGCCATTGATTCAGAAATGGATGGTGCTAGTGAGATTGAATTAGCATTCAGGCCTCAACCCACATTTATAGAAA
AGGATGATAGTGCACAGATAAGATACATAAAGACTTCAGGTAACACTGCTGTTGATCACTTATCCAGGTATCTGACTGTG
AGGTTAGCTTTAGAAGAACTTTGAAGCCAAGGTGCATAAGACCAGATGAAC

Alignment

ORF - retro_pabe_3374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.93 %
• Parental protein coverage: 52.68 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FDALISKIYPSRDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGD
          FDALISKIYP..D.YEA...RVLA.I.KH.NQ.ALS.S..EGLK.....RLQ.GKKQ..ENGS.AE.N.D
Retrocopy FDALISKIYPGHDKYEALGDRVLASIHKHSNQ*ALSLSSKEGLKVPVRSRLQ*GKKQ*TENGSRAEENAD

Parental  SSHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASEIELVFRPHPTLMEKDDSAQT
          ..HCS.AST..N.E.G.S.K.TKTS.DSGLELD..NA..AID..MDGASEIEL.FRP.PT..EKDDSAQ.
Retrocopy GLHCSGASTQNNKETGHSHKWTKTSADSGLELDIDNATFAIDSEMDGASEIELAFRPQPTFIEKDDSAQI

Parental  RYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMN
          RYIKTSGN..VDHLS.YL.VRLALEEL.S.G...QMN
Retrocopy RYIKTSGNTAVDHLSRYLTVRLALEEL*SQGA*DQMN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.73 RPM
SRP007412_cerebellum	0.00 RPM	7.54 RPM
SRP007412_heart	0.00 RPM	4.61 RPM
SRP007412_kidney	0.00 RPM	4.31 RPM
SRP007412_liver	0.00 RPM	1.68 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3374 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3374 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011199	3 retrocopies	retro_chof_1450, retro_chof_2217, retro_chof_2251,
Callithrix jacchus	ENSCJAG00000005442	1 retrocopy	retro_cjac_4198,
Erinaceus europaeus	ENSEEUG00000014091	1 retrocopy	retro_eeur_88,
Echinops telfairi	ENSETEG00000015824	1 retrocopy	retro_etel_2081,
Felis catus	ENSFCAG00000009609	1 retrocopy	retro_fcat_1725,
Homo sapiens	ENSG00000121481	2 retrocopies	retro_hsap_4056, retro_hsap_4226,
Gorilla gorilla	ENSGGOG00000014400	1 retrocopy	retro_ggor_2724,
Loxodonta africana	ENSLAFG00000021357	1 retrocopy	retro_lafr_407,
Myotis lucifugus	ENSMLUG00000001129	1 retrocopy	retro_mluc_2187,
Monodelphis domestica	ENSMODG00000007422	1 retrocopy	retro_mdom_857,
Nomascus leucogenys	ENSNLEG00000018029	2 retrocopies	retro_nleu_1042, retro_nleu_554,
Oryctolagus cuniculus	ENSOCUG00000004892	1 retrocopy	retro_ocun_838,
Pongo abelii	ENSPPYG00000000417	2 retrocopies	retro_pabe_3331, retro_pabe_3374 ,
Pan troglodytes	ENSPTRG00000001775	2 retrocopies	retro_ptro_2749, retro_ptro_2871,
Ictidomys tridecemlineatus	ENSSTOG00000006625	3 retrocopies	retro_itri_1646, retro_itri_1794, retro_itri_410,
Tupaia belangeri	ENSTBEG00000016387	4 retrocopies	retro_tbel_1757, retro_tbel_3368, retro_tbel_3892, retro_tbel_4061,
Tarsius syrichta	ENSTSYG00000006109	6 retrocopies	retro_tsyr_1344, retro_tsyr_1647, retro_tsyr_2063, retro_tsyr_2083, retro_tsyr_227, retro_tsyr_474,