Sequence
atgc intronic sequence ATGC exonic sequencegtttgtggtgacttgatatatcaaggaattttcttctactagtttgtgattccctttgagtgaatattttaaaggtttttccttggtctgttgaattgagtttgatgtggttttctttcgaatatcacattaaagGTTAAAGAATGGCTTCAAAATCTAGGAATAGGGGATCATCCACCCGTTGTGCAAGATGAAGATGCTGATGAAGTTCCGCTACATCAAGATGAAAGTGCCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16785.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G343588_T01 (Zea mays), 3'ss of exon 2
gtttgtggtgacttgatatatcaaggaattttcttctactagtttgtgattccctttgagtgaatattttaaaggtttttccttggtctgttgaattgagtttgatgtggttttctttcgaatatcacattaaagGTTAAAGAATGGCTTCAAAATCTAGGAATAGGGGATCATCCACCCGTTGTGCAAGATGAAGATG---CTGATGAAGTTCCGCTACATCAAGATGAAAGTGCCA
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----------atttgac-tgtcaac---tcttcttgacacagtat---atttgttttgtgcggaagcttca-------tttccagtcatgtagaactgaact------aatctccttt-----gtttaattaaagGTCAAAGAATGGCTTCAAAATTTGGGGATAGGGGAGCATGTGCCAGTTGTACATGATGATGATGAAGCCGATGATGTGCATGTTCCTTCACAGCATGACG---
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 2
------------gtttgtggtgacttgatatatcaaggaattttcttctactag--tttgtgattccctttgagtgaatattttaaaggtttttccttggtct-gttgaatt--gagtttgatgtggttttctttcgaatatcacattaaagGTTAAAGAATGGCTTCAAAATCTAGGAATAGGGGATCATCCACCCGTTGTGCAAGATGA------AGATGCTGATGAAGTTCCGCTACATCAAGATGAAAGTGCCA
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gtgagcaatgttgtttacattgattttcggt-tgattgccttatatatgaatggattttgtgcgcatttattgtattattttttggtgatatcatttctatctagctaagtttggattttgatgtaatgttcactgaaacattatattaaagGTTAAAGAATGGCTTCAAAATCTAGGAATTGGAGAACACACTGCTATGGCGCAAGATGACGACGAAGGTGATGATGAGACTGTCCCGTTGCATACTGAAG------
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 2
------------gtttgtggtgacttgatatatcaaggaattttcttctactagtttgtgattccctttgagtgaatattttaaaggtttttccttggtct-gttgaatt--gagtttgatgtggttttctttcgaatatcacattaaagGTTAAAGAATGGCTTCAAAATCTAGGAATAGGGGATCATCCACCCGTTGTGCAA------GATGAAGATGCTGATGAAGTTCCGCTACATCAAGATGAAAGTGCCA
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gtgagcaatgttgtttatattgatttttggt-tgattgccttatatatgaatggattttgtgcatttattatattattttttggtgatatcatttctatctagctaagtttggattttgatgtaatgttcactgaaacattatattaaagGTTAAAGAATGGCTTCAAAATCTAGGAATTGGAGAACACACTGCTATGGTGCAAGATGACGATGAAGGTGATGATGAAACTGTCCCGTTGCATACTGAAG------
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 2
gtttgtggtgacttgatatatcaaggaattttcttctactagtttgtgattccctttgagtgaatattttaaaggtt-tttccttggtctgttgaattgagtttgatgtggttttctttcgaatatcacattaaagGTTAAAGAATGGCTTCAAAATCTAGGAATAGGGGATCATCCACCCGTTGTGCAAGATGAAGATG---CTGATGAAG------TTCCGCTACATCAAGATGAAAGTGCCA
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--gtgtgcttcattcttttttccttgttttttattgtatctgataacg-taagttcgggaagattctcccatttattgtttagttgggaaggtgtggggtttttgatatagtttttattt-aacat----ttaaagGTTAAAGAATGGCTTCAAAACATAGGAATAGGAGAGCACACAGCAGTCGTGCATGATGATGATGAACCTGATGAGGAAACTGTTCCTTTACATCATGATG--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttggtctgttgaattgagtttgatgtggttttctttcgaatatcacattaaagGTTAAAGAATGGCTTCAAAATCTAGGAATAGGGGATCATCCACCCGTTGTGCAAGATGAAGATGCTGATGAAGTTCCGCTACATCAAGATGAAAGTGCCA
gtttgat putative branch site (score: 5)
aatatcacattaaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtggtgacttgatatatcaaggaattttcttctactagtttgtgattccctttgagtgaatattttaaaggtttttccttggtctgttgaattgagtttgatgtggttttctttcgaatatcacattaaagGTTAAAGAATGGCTTCAAAATCTAGGAATAGGGGATCATCCACCCGTTGTGCAAGATGAAGATGCTGATGAAGTTCCGCTACATCAAGATGAAAGTGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG