RetrogeneDB ID: retro_ocun_1834

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019190:89893..90714(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFPQ
• Ensembl ID: ENSOCUG00000001877
• Aliases: None
• Description: splicing factor proline/glutamine-rich [Source:HGNC Symbol;Acc:10774]

Sequence

>retro_ocun_1834
GAAGGTGTTTTCTTACTGACAGCAGCTCCTCTTCCAGTCATTGTGGAACCACTCAAACAGTTAGATGACAAAGATGGTCT
TCCTGAGAAGTTTGCACAGAAGAATCCGATGTATCAGAAGGAGAGAGAAACTCCTCCACACTTTGCTCAGCATGGTACGT
TTGAATATGAATACTCTCAGCGATGGAAGTCTTGGATGAATGGAGAAACAGCAGAGGGAACAAGTTGAAAAAAATATGAA
GGATGCAAAAGATAAATTGGAAAGTGAAATGGAAGATGCCTATCTTGAGCATCAGGCAAATCTTTTGCGCCAAGATCTAA
TGAGACATCAGGAAGAATTAAGACATGGAAGAACTTCACAATCAAGAAATGCAGAAATGTAAAGAAATGTAATTGAGGCA
TGAGGAAGAACGATATAGAAAGGAGGAAGAGGTGATGATTCATCAACATGAGATGGAAGAACAAATGAGACGCCAAAGGG
AGGAAAGTTACAGTCCTATGGGCTACCTGGATCCAAGAGAAAGAGACATGAGAATGGGAGGTGGAGGAGCGATGATGATG
GGAGACCCCTATGGTTCAGGAGGCCAGAAATTTTCACCTCTAGGTGGTGGTGGTGGCATAGGTTATGAAGCTAACCCTGG
AGTTCCACGAGCAACCATGAGTGGTTCCATGATGGGAAGCGACATGCGTACTGAGTGCTTTGGACAGGGAGGTGCAGGGC
CTGTGGGTGGACAGGGTCCTAGAGGAATGGGGCCTGGAACTCCAGCAGGATATGGTAGAGGGAGAGAAGAGTATGAAGGC
CCCAACAAAAAGCCCCAATTT

Alignment

ORF - retro_ocun_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.85 %
• Parental protein coverage: 54.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EGVFLLTTTPRPVIVEPLEQLDDEDGLPEKLAQKNPMYQKERETPPRFAQHGTFEYEYSQRWKS-LDE-M
          EGVFLLT..P.PVIVEPL.QLDD.DGLPEK.AQKNPMYQKERETPP.FAQHGTFEYEYSQRWKS.LDE.M
Retrocopy EGVFLLTAAPLPVIVEPLKQLDDKDGLPEKFAQKNPMYQKERETPPHFAQHGTFEYEYSQRWKS<LDE<M

Parental  EKQQREQVEKNMKDAKDKLESEMEDAYHEHQANLLRQDLMRRQEELRR-MEELHNQEMQKRKEMQLRQEE
          EKQQREQVEKNMKDAKDKLESEMEDAY.EHQANLLRQDLM.R..E..R.MEELHNQEMQK.KEM.LR.EE
Retrocopy EKQQREQVEKNMKDAKDKLESEMEDAYLEHQANLLRQDLM-RHQEELR>MEELHNQEMQKCKEM*LRHEE

Parental  ERRRREEEMMIRQREMEEQMRRQREESYSRMGYMDPRERDMRMGGGGAMNMGDPYGSGGQKFPPLGGGGG
          ER.R.EEE.MI.Q.EMEEQMRRQREESYS.MGY.DPRERDMRMGGGGAM.MGDPYGSGGQKF.PLGGGGG
Retrocopy ERYRKEEEVMIHQHEMEEQMRRQREESYSPMGYLDPRERDMRMGGGGAMMMGDPYGSGGQKFSPLGGGGG

Parental  IGYEANPGVPPATMSGSMMGSDMRTERFGQGGAGPVGGQGPRGMGPGTPAGYGRGREEYEGPNKKPRF
          IGYEANPGVP.ATMSGSMMGSDMRTE.FGQGGAGPVGGQGPRGMGPGTPAGYGRGREEYEGPNKKP.F
Retrocopy IGYEANPGVPRATMSGSMMGSDMRTECFGQGGAGPVGGQGPRGMGPGTPAGYGRGREEYEGPNKKPQF

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	0.06 RPM	147.19 RPM
SRP017611_kidney	0.00 RPM	114.03 RPM
SRP017611_liver	0.08 RPM	42.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1834 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1834 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003595	1 retrocopy	retro_cfam_198,
Callithrix jacchus	ENSCJAG00000001431	4 retrocopies	retro_cjac_1073, retro_cjac_2542, retro_cjac_2697, retro_cjac_486,
Felis catus	ENSFCAG00000031287	1 retrocopy	retro_fcat_1989,
Gasterosteus aculeatus	ENSGACG00000002034	1 retrocopy	retro_gacu_13,
Gadus morhua	ENSGMOG00000011950	1 retrocopy	retro_gmor_20,
Macropus eugenii	ENSMEUG00000014082	1 retrocopy	retro_meug_164,
Oryctolagus cuniculus	ENSOCUG00000001877	1 retrocopy	retro_ocun_1834 ,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317, retro_ocun_1804,
Oreochromis niloticus	ENSONIG00000017737	1 retrocopy	retro_onil_21,
Sarcophilus harrisii	ENSSHAG00000016107	1 retrocopy	retro_shar_36,
Tetraodon nigroviridis	ENSTNIG00000011331	1 retrocopy	retro_tnig_32,
Takifugu rubripes	ENSTRUG00000003783	1 retrocopy	retro_trub_8,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,