RetrogeneDB ID: retro_itri_867

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393335.1:4292068..4292748(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000026267
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_867
CATCTCACAGCCTTTCTGGGATACAAGGCTGGCATGACCTATATCAAGTGGGAAGTTGATAAGCCAGGATCCAAGGTGAA
CAAGGAGGAGGTTGTGGAGGTTGTAATCATAGAGGAGACACCACCCAGGGTGGTTATAGGCATTGTGAGCTACGTGGAAA
CCCTACCAGGCCTCCAGTCCTTCAAGACCATCTTTGCTGAGCATATCAGTGATGAGTGCAAAAGGTGCTTCTATAAGAAC
TGGCATAAATCTAAGAAGAAGGCCTTTGCCAAATACTGCAAGAAGTGGCAGGATGTAATGGGCAAGAAGCAATTGGAGAA
GGACTTCAGCATGAAAAAATACTGCCAGGACATCCAGATTATCGCCTCCACCCAGATGTGGCTGCTTCCCTTGCACCAGA
AGAAAGCCCGCCTGATGGAGTTCCAGGTGAATGGAGGCACCAAGGCTAAGAAACTGAACTGGGCCAGGAGAGGCTGGAGC
AGCAGGTCCCAATGAACCAGGTGTTTGGGCAGGATGACATGATGGATATCATCAGTGTGACCAAGGGCAAAGGCTACAAA
GGAGTCACCAGTCACTGGCATACCAAGAAGCTGCCCGGCAAGACCCACCAAGGGCTGTGCAAGGTTGCCTGTATTGGAGC
TTGGCATCCTGCCTATGTGGTCTTCTCTGTGACCTGGGCT

Alignment

ORF - retro_itri_867 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.94 %
• Parental protein coverage: 56.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HLTAFLGYKAGMTHTLREVHRPGLKISKREEVEAVTIVETPPLVVVGVVGYVATPRGLRSFKTIFAEHLS
          HLTAFLGYKAGMT....EV..PG.K..K.E.VE.V.I.ETPP.VV.G.V.YV.T..GL.SFKTIFAEH.S
Retrocopy HLTAFLGYKAGMTYIKWEVDKPGSKVNKEEVVEVVIIEETPPRVVIGIVSYVETLPGLQSFKTIFAEHIS

Parental  DECRRRFYKDWHKSKKKAFTKACKRWRDTDGKKQLQKDFAAMKKYCRVIRVIVHSQMKLLPFRQKKAHIM
          DEC.R.FYK.WHKSKKKAF.K.CK.W.D..GKKQL.KDF..MKKYC..I..I...QM.LLP..QKKA..M
Retrocopy DECKRCFYKNWHKSKKKAFAKYCKKWQDVMGKKQLEKDF-SMKKYCQDIQIIASTQMWLLPLHQKKARLM

Parental  EIQLNGGTVAEKVAWA-QARLEKQVPVHSVFSQSEIIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRK
          E.Q.NGGT.A.K..WA.Q.RLE.QVP...VF.Q....D.I.VTKG.G.KGVTS.WHTKKLP.KTH.GL.K
Retrocopy EFQVNGGTKAKKLNWA<QERLEQQVPMNQVFGQDDMMDIISVTKGKGYKGVTSHWHTKKLPGKTHQGLCK

Parental  VACIGAWHPARVGCSIARA
          VACIGAWHPA.V..S...A
Retrocopy VACIGAWHPAYVVFSVTWA

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_867 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_867 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 ,