Sequence
atgc intronic sequence ATGC exonic sequencegtacgtacggttgagatttcttttaactattctattgatttgattgtgttgcttacaataattaagcatattaataatatatgtgtgtttccgtgattgtgaagGAAGAAGATAACGAAATTCCCGAGGTTTAGGCTATGGACATTTCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G49740.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G49740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G068557_T01 (Zea mays), 3'ss of exon 2
gtacgtacggttgagatttcttttaactattctattgatttgattgtgttgcttacaataattaagcatattaataatatatgtgtgtttccgtgattgtga---agGAAGAAGATAACGAAATTCCCGAGGTTTAGGCTATGGACATTTCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
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-------agagcagaaccttgcataatttttacatagatttcctgctcctgcttccggttcatgtacactattctagtattcatctctacttttacttgcgcgccagGAAAAGGAAGCTGCGCTCACTGAGTTTCAGGCTCTGGACTTTCCCTGTTCTTGTAGACGGCCCCTTTGGAGTTGTCTCTGCAGTTGAGTTCATCGGAATT
upper sequence: AT5G49740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G13090.1 (Glycine max), 3'ss of exon 2
--gtacgtacggttgagatttcttttaactattctattgatttgattgtgttgct-tacaata-attaagcatattaataatatatgtgtgtttccgtgattgtgaagGAAGAAGATAACGAAATTCCCGAGGTTTAGGCTATGGACATTTCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
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ttgaagttgcggccgaaattgcggtca--caggcggatttttaaaacatgacattatagtatatgttgagtactttgtttttg-acttgggttttgatggc-----agGAAGAAGACGTCCAAACTTCCAAGGTTTCGCCTATGGACATTTCCTGTGCTTGTGAAGGGACCATTTGGGGTTGTTTCTGCCACAGAGCTTATTGGGATT
upper sequence: AT5G49740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G02170.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------------gtacgtacggttgagatttcttttaactatt-ctattgatttgattgtgttgcttacaataattaagcatattaa-taatatatgtgtgtttccgtgattgt--gaagGAAGAAGATAACGAAATTCCCGAGGTTTAGGCTATGGACATTTCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
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gtatgtgatttcctcaaacttacctttctgtgcacaacatttcatcatcattatagcaaggttttcaattaccgtcacagtttcgacaca-atctttgatattgcgggaaattgtggtcacagacagatttttgaaacctggcattatagtatatgttgagtactttgtttttgatttggaatttgatggcagGAAGAAGACTTCCAAACTTCCAAGGTTCCGCCTATGGACGTTTCCTGTGTTTGTGAAGGGACCATTTGGGGTTGTTTCTGCCACAGAGCTTATTGGGATT
upper sequence: AT5G49740.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0035g02150.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtacgtacggttgagatttcttttaactatt-----ctattgatt-------tgattgt-----gttgcttacaataattaagcatattaataatatatgtgtgtttccgtga----ttg--tgaagGAAGAAGATAACGAAATTCCCGAGGTTTAGGCTATGGACATTTCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
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gtatgtgatctatagtgtgataaattatgtcttcttatctccaatgctatctgctgagtgaacacatgctcattactggtttctttctataat-agttgtcctagttttttctttctcatcatataaaactttggttatagGAAGAGGACTTCCAACTGTCCAAGATTTCGGTTGTGGACTTTTCCTGTTCTTGTGGATGGACCTTTTGGAGTGGTCTCTGCTGCTGAGTTCATCGGGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttacaataattaagcatattaataatatatgtgtgtttccgtgattgtgaagGAAGAAGATAACGAAATTCCCGAGGTTTAGGCTATGGACATTTCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
tattaat putative branch site (score: 2)
aataattaagcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtacggttgagatttcttttaactattctattgatttgattgtgttgcttacaataattaagcatattaataatatatgtgtgtttccgtgattgtgaagGAAGAAGATAACGAAATTCCCGAGGTTTAGGCTATGGACATTTCCTGTTCTTGTGGATGGACCATTTGGAGTTGTTTCTGCAGCTGAGTTTCTTGGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA