RetrogeneDB ID: retro_rnor_2822

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:75735487..75736201(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sf3a2
• Ensembl ID: ENSRNOG00000019349
• Aliases: None
• Description: Splicing factor 3A subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:Q6AXT8]

Sequence

>retro_rnor_2822
CAAGGCGAGCTGCCAAGGAGGTCAAAGAAGTCCCCCCCCCCCGCCCAGCCTGCACCCGTGAAGGTCAAGATGAAAGTGAA
GAAATTTGTGAAGGTTGGCCGCCCTAGCTACAAAGTGGCCAACCAGAGGGACACAGAGATGGGCCAGCAGAGCCTGCTGT
TCCAGATTGACTACCCTGAGATTGCAGAGGGCATCATGCTACGCCACTGCTTCATGTCTGACTATGAGCAGAGGGGTCAA
GCCCCTGAACCACCGCTGGTAGTATGTGCTCATGGCTGCTGAGCCCTATGAGACCATTGACTTCAAGGTGTTGAGCCGGG
AGATTGACAAGGCTGAGGGCAAGTTTTGGACCCACTGGTGCCGAGAGACCAAGCAGTTTTTTCTTCAGTTCCATTTTAGG
ATGAAGAAGCCCCGGACCCCTCCCAGCCTCCCAGCAGGATCCCCAGGCATCAAGCAGCCCCCACCCCCACTCATGAATGA
ACTGACTCCTTGTCCATCACTCCCTGAAGCCTTGGCCCCACCTCCACCTGGTGGCCTGCTTCTTCTTCCTATGCTCCCAC
TGGGCCTGCTCCCTCTGGGCCCCCTGGACCTCCCCAAATGCCCCACCACCTCCTGGAGTGCACCCCCAACCCCAGTATTA
CACCCACCTACATCTGGAGTCCATTCCCAAGCTCCTAGGGTACACCCCCAGCACCAGTGGTCCATCCACCATCT

Alignment

ORF - retro_rnor_2822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.67 %
• Parental protein coverage: 51.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVTKQRDTEMGQQSLLFQIDYPEIAEGVMPR
          Q..L.RR..K....A..QPAP.KVK..VKKFVK.GRP.YKV..QRDTEMGQQSLLFQIDYPEIAEG.M.R
Retrocopy QGELPRRSKKXXXXA--QPAPVKVKMKVKKFVKVGRPSYKVANQRDTEMGQQSLLFQIDYPEIAEGIMLR

Parental  HRFMSAYEQR-IEPPDRRWQYLLMAAEPYETIAFKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKP
          H.FMS.YEQR...P...RW.Y.LMAAEPYETI.FKV.SREIDKAEGKFWTHW.RETKQFFLQFHF.M.K.
Retrocopy HCFMSDYEQR>VKPLNHRW*YVLMAAEPYETIDFKVLSREIDKAEGKFWTHWCRETKQFFLQFHFRMKKX

Parental  PAPPSLPAGPPGVKRPPPPLMNGLPPRPPLPDALPPPPPGGLPLPPMPPTGPAPSGPPGPPQMP-PPAPG
          ...................LMN.L.P.P.LP.AL.PPPPGGL.L.P..............P..P.PP.PG
Retrocopy XXXXXXXXXXXXXXXXXXXLMNELTPCPSLPEALAPPPPGGLLLLPXXXXXXXXXXXLDLPKCP>PP-PG

Parental  VH-PPAPVVHPPTSGVHPPAPGVH-PPAPVVHPPT
          VH.PP.PV.HPPTSGVH..AP.VH.PPAPVVHPP.
Retrocopy VH<PPTPVLHPPTSGVHSQAPRVH<PPAPVVHPPS

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	19.77 RPM
SRP017611_kidney	0.00 RPM	17.93 RPM
SRP017611_liver	0.00 RPM	12.04 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2822 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2822 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2822 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013206	4 retrocopies	retro_cjac_1621, retro_cjac_2029, retro_cjac_3563, retro_cjac_3971,
Otolemur garnettii	ENSOGAG00000033389	2 retrocopies	retro_ogar_3423, retro_ogar_3439,
Rattus norvegicus	ENSRNOG00000019349	1 retrocopy	retro_rnor_2822 ,