RetrogeneDB ID: retro_itri_1344

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393446.1:611223..612084(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3L
• Ensembl ID: ENSSTOG00000012921
• Aliases: None
• Description: ribosomal protein L3-like [Source:HGNC Symbol;Acc:10351]

Sequence

>retro_itri_1344
CCAGGATCCAAAGTGAACAAGAAGGAAGATGTAAAGACTGTGACCACTGTGGAGACGCCACGTGGGGCAATTGTAGGAAC
TGTGTGTTCTATGGAAACCTCTGGAGGCCTCAGGACCTACAAGACCATCTTTGCAGAGTACATTAGTGCACACGATCACT
TACATAAGAACTGGCATAGACCTAAGAAGAAGGCCTTCACCAAATTCTGCAAGAAATGGCAGGATGACAGGGACAAGAAG
CAGCTAAAGAAGGACTTTAGCAGCTTGAAGTACTGCCAGATCATCTGCATTATTGCCCACCCTCAGGTGCACCTGCTTAC
TATATGCCAGAAGGTCCACCTGATGGAGATCCAGGTGATTAAGGGATATTGTGGCCCATAAACTTGACTGATTTCAGGAG
AGGCTGGAGCAGCATGTCCCAATGAACCAGGTGCTTGGGCAGGATAAGATAATCAATGTCACTGGGGTTACCAAAGGCAA
ACGTTACAAAGGAGTCACCAGTCACTGGCACATCAAGAAACTGCCCCATAAGACCCACTGAGGGTTGTGCTAGATTGCCT
TATTGGAGCATGACACCCTGCCCATATGGCCTTCTCTATGGCAAAGGTTAGACAGAAGGCTACTGTCACCACACTGAGAT
CAACAAGATCTACAAGAATGATCAAGGCTGCCTTTTGAGGACAGCAAGCTGATGAAGAACAATGCCTCCACTGACGATAC
TTGTCTGAAAAGAGGATCAATCCTCTGGATGGTTTTATCCACAATGGTGAAGTGACCTGATGACTTTGTCATCCTGAAAG
CTGTGTGGTGGGATCCAAAAAGCAGTTGCTCACCTTCTATATGTCCTTGCTGATAAGGCAC

Alignment

ORF - retro_itri_1344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.33 %
• Parental protein coverage: 72.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  PGLKISKREEVEAVTIVETPPLVVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFTK
          PG.K..K.E.V..VT.VETP....VG.V....T..GLR..KTIFAE..S........K.WH..KKKAFTK
Retrocopy PGSKVNKKEDVKTVTTVETPRGAIVGTVCSMETSGGLRTYKTIFAEYIS--AHDHLHKNWHRPKKKAFTK

Parental  ACKRWRDTDGKKQLQKDFAAMKKYCRVIRVIVHSQMKLLPFRQKKAHIMEIQLNGG-TVAEKVAWAQARL
          .CK.W.D...KKQL.KDF...K.YC..I..I.H.Q..LL...QK..H.MEIQ...G..VA.K....Q.RL
Retrocopy FCKKWQDDRDKKQLKKDFSSLK-YCQIICIIAHPQVHLLTICQK-VHLMEIQVIKG>IVAHKLD*FQERL

Parental  EKQVPVHSVFSQSEIIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVA-CIGAWHPARVGCSIARAG
          E..VP...V..Q..II.V..VTKG...KGVTS.WH.KKLP.KTH.GL...A..IGA.HPA....S.A...
Retrocopy EQHVPMNQVLGQDKIINVTGVTKGKRYKGVTSHWHIKKLPHKTH*GLC*IA<LIGA*HPAHMAFSMAKVR

Parental  QK-GYHHRTELNKKIYRIGRG-LHMEDGKLVKNNASTSYD-VTDKSITPLGGFPHYGEVN-NDFVMLK-G
          QK.GY.H.TE.N.KIY....G.L..ED.KL.KNNAST.......K.I.PL.GF.H.GEV...DFV.LK..
Retrocopy QK<GYCHHTEIN-KIYKNDQG<LPFEDSKLMKNNASTDDT<LSEKRINPLDGFIHNGEVT>DDFVILK<S

Parental  CIAGTKKRVITLRKSLLVHH
          C..G.KK...T...SLL..H
Retrocopy CVVGSKKQLLTFYMSLLIRH

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1344 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1344 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 5 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008489	1 retrocopy	retro_amel_1881,
Nomascus leucogenys	ENSNLEG00000008850	9 retrocopies	retro_nleu_1107, retro_nleu_1130, retro_nleu_1249, retro_nleu_1305, retro_nleu_1673, retro_nleu_1824, retro_nleu_2046, retro_nleu_2060, retro_nleu_3126,
Pongo abelii	ENSPPYG00000006973	1 retrocopy	retro_pabe_2854,
Pan troglodytes	ENSPTRG00000007617	12 retrocopies	retro_ptro_1439, retro_ptro_1473, retro_ptro_1753, retro_ptro_2150, retro_ptro_2339, retro_ptro_2462, retro_ptro_2501, retro_ptro_2646, retro_ptro_2741, retro_ptro_2767, retro_ptro_3163, retro_ptro_916,
Ictidomys tridecemlineatus	ENSSTOG00000012921	2 retrocopies	retro_itri_1344 , retro_itri_867,