RetrogeneDB ID: retro_rnor_2350

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:35074441..35075235(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sf3b4
• Ensembl ID: ENSRNOG00000021181
• Aliases: None
• Description: Splicing factor 3B subunit 4 [Source:UniProtKB/Swiss-Prot;Acc:Q6AYL5]

Sequence

>retro_rnor_2350
GCTAACTATGCCATTCAGATTATGAACATGATCAAACTCTATGGGAAGCCAATATGGGTGAACAAGGCCTCGGGTCACAA
CAAAAACCTGGATTTAGAAGCCAACATTTTCATGGGAAACCTGGATCCAGAAATTAATGAAAAGCTGCCTTCAATACATT
TACGATACTTCCAAGGCATTTGGAGCCACCTTAAAGACCCCCCAAGATTATGCGGGGCCCTGACACAGGCTACTCCAAGG
TTATGCCTTCAGTAATTTTGCTTCATTTGATGCTTCGGATGCAGCAGTTGAAGCCATGAACCTGTGTAACTGCCCTGTCA
CTGTGTCTTAGGCTTTCAAGAAGGACTCTAAGGGTAAACGCCATGACTCAGCAGCTGAACAACTTCTGGCAGCCCAGAAC
CCACTGTCCCAGGCTAACCACCCTCATCAGCTGTTTGCTGATGTACCCCCCTCCACCCTCTGCCACCAATTCTCAGGTTT
CATCCCTGGGTTTTGGGCTTCCTTCACCAGGCATGCCATCTCCTGAGTCGTTCCCATCTCCAGTGCCACTTCTTGGGGCC
CTCCCTCCTGGGAAACCTCTAACCATTCCCCCGCCACCTGTGCCACGTGGAGCTAGAGGACATGGTCCCCCAGCAGCAGG
GGCTGAACATCCGGGTCAAGGACATTCATTTCCTCTACCATTCCCACCAGGTGGGATGCCCCATCTGGGGATGTCCCAGA
TGCAGCTGGACCACCATGGCCCCCATGACCTAGGACACCTCCATGCTTGGCCTTCAGGCTCTAGGGGGCAGCCA

Alignment

ORF - retro_rnor_2350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.36 %
• Parental protein coverage: 62.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ADYAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKL-LYDTFSAFGVILQTP----K
          A.YAI.IMNMIKLYGKPI.VNKAS.HNKNLD..ANIF.GNLDPEI.EKL....TF......L..P....K
Retrocopy ANYAIQIMNMIKLYGKPIWVNKASGHNKNLDLEANIFMGNLDPEINEKL<AFNTFTILPRHLEPP*RPPK

Parental  IMRDPDTGNSK-GYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNP
          IMR.PDTG.SK.GYAF.NFASFDASDAA.EAMN...LCN.P.TVS.AFKKDSKG.RH.SAAE.LLAAQNP
Retrocopy IMRGPDTGYSK<GYAFSNFASFDASDAAVEAMN---LCNCPVTVS*AFKKDSKGKRHDSAAEQLLAAQNP

Parental  LSQADRPHQLFADA-PPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPG
          LSQA..PHQLFAD..PPPPSA.N..VSSLG.GLP.PGMP.P.SFP.PVP..GALPPG.P...PPPP.P.G
Retrocopy LSQANHPHQLFADV>PPPPSATNSQVSSLGFGLPSPGMPSPESFPSPVPLLGALPPGKPLTIPPPPVPRG

Parental  AGGHGPPAAGTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQP
          A.GHGPPAAG...A.HPG.GHS.P.PFPPGGMPH.GMSQMQL.HHGPH.LGH.HA.P.GS.GQP
Retrocopy ARGHGPPAAG---AEHPGQGHSFPLPFPPGGMPHLGMSQMQLDHHGPHDLGHLHAWPSGSRGQP

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
SRP017611_brain	0.00 RPM	25.81 RPM
SRP017611_kidney	0.00 RPM	35.45 RPM
SRP017611_liver	0.00 RPM	10.49 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2350 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2350 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012495	2 retrocopies	retro_btau_1385, retro_btau_592,
Canis familiaris	ENSCAFG00000011617	3 retrocopies	retro_cfam_585, retro_cfam_711, retro_cfam_729,
Callithrix jacchus	ENSCJAG00000000793	3 retrocopies	retro_cjac_1297, retro_cjac_1909, retro_cjac_638,
Cavia porcellus	ENSCPOG00000008267	1 retrocopy	retro_cpor_234,
Echinops telfairi	ENSETEG00000008963	1 retrocopy	retro_etel_1310,
Homo sapiens	ENSG00000143368	1 retrocopy	retro_hsap_1356,
Gorilla gorilla	ENSGGOG00000004761	1 retrocopy	retro_ggor_1056,
Macaca mulatta	ENSMMUG00000007256	1 retrocopy	retro_mmul_2191,
Mustela putorius furo	ENSMPUG00000005563	2 retrocopies	retro_mputfur_1105, retro_mputfur_648,
Oryctolagus cuniculus	ENSOCUG00000004614	1 retrocopy	retro_ocun_1239,
Pongo abelii	ENSPPYG00000000912	1 retrocopy	retro_pabe_1124,
Pan troglodytes	ENSPTRG00000001243	1 retrocopy	retro_ptro_930,
Pteropus vampyrus	ENSPVAG00000014171	1 retrocopy	retro_pvam_931,
Rattus norvegicus	ENSRNOG00000021181	1 retrocopy	retro_rnor_2350 ,
Ictidomys tridecemlineatus	ENSSTOG00000000684	2 retrocopies	retro_itri_1153, retro_itri_487,