Sequence
atgc intronic sequence ATGC exonic sequence...ttgttgtcacatctgagggagatcagttagtaacagttggattttgattcaagtaaaaccgctcattctggtcacatctgaacgttcttgttcatcgcagGTAGTGATGCCTACAGTGGAAGCTGATGTGGCATTTGGTCTTGGCAAGTATCATGACATGAATCAGGAAGAAGTTAAGTCTAGGGTGATTAAAGCTTTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g56400.1 (Oryza sativa), 3'ss of exon 2
----ttgttgtcacatctgagggagatcagttagtaacagttggattttgattcaagtaaaaccgctcattctggt-cacatctgaacgttcttgttcatcgcagGTAGTGATGCCTACAGTGGAAGCTGATGTGGCATTTGGTCTTGGCAAGTATCATGACATGAATCAGGAAGAAGTTAAGTCTAGGGTGATTAAAGCTTTGG---
| ||| ||| |||| |||| ||| | ||| | || | | | | | || | ||||||| || || | || | |||||| |||||||| ||||||||| | ||||| |||||||||||||| ||| | || | ||| || |||| ||| || || || | |||
ttgactcttgatgcattggaggaagattgcttaatgacacattcatgtcaaattagatcaagct-----ttctggtacatattaagttacgttctttgaatgcagGTTGTGATGCCGACAGTGGAATCAGATGTTGCATTTGGTCTTGGTAAG---CTCAACCTTTCGTTGGATGAGGTTAGGTCAAGAGTATCACAATCACTGGATG
upper sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G111511_T02 (Zea mays), 3'ss of exon 2
-ttgttgtcacatctgagggagatcagttagtaacagttggattttgattcaagtaaaaccgctcattctggtcacatctgaacgttcttgttcatcgcagGTAGTGATGCCTACAGTGGAAGCTGATGTGGCATTTGGTCTTGGCAAGTATCATGACATGAATCAGGAAGAAGTTAAGTCTAGGGTGATTAAAGCTTTGG---
| || || | || | | || | || | | | | | || | | | || || |||||| |||||||||||||||| | ||||||| ||||||||||| || ||| ||| || | | || | || || | || ||||| ||| ||||||
ataactgcaaccccagactgttcatgtgcccaagtctttataccatgtctttatatggaagaacgactgtgattttct-tagttgtgtcctttggatgcagGTTGTGATGCCTACAGTGGGATCTGATGTAGCATTTGGTCTCGGTAAGC-TCA-AACTTCCGTTAG-ATGAGGTCAGGTTAAGGGTATCAAAATCTTTGGATG
upper sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0044g01320.t01 (Vitis vinifera), 3'ss of exon 3
ttgttgtcacatctgagggagatcagttagtaacagttggattttgat-tcaagtaaaaccgctcattctggtcacatctgaacgttct-tgttcatcgcagGTAGTGATGCCTACAGTGGAAGCTGATGTGGCATTTGGTCTTGGCAAGTATCATGACATGAATCAGGAAGAAGTTAAGTCTAGGGTGATTAAAGCTTTGG---
| || || | | | | || |||| | || | | || | | | | | | ||| | | ||| ||||| ||||||||||||||||||||| ||||| ||||| |||||||| ||||| |||| ||| || ||| |||||||| | ||| || ||| |||||| |||
tagtaacagaatagatgacatgttcatgcgtctttgttgaagcttaacatgaaattctcacatttaattttatcaaggcaacatcttccatgttc--tgcagGTAGTGATGCCTACAGTAGAAGCAGATGTTGCATTTGGCCTTGGTAAGT-TCA--ACCTGACAATTGAAGAAGTCAGGTCAAGAGTGTCGAAAGCTCTGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattcaagtaaaaccgctcattctggtcacatctgaacgttcttgttcatcgcagGTAGTGATGCCTACAGTGGAAGCTGATGTGGCATTTGGTCTTGGCAAGTATCATGACATGAATCAGGAAGAAGTTAAGTCTAGGGTGATTAAAGCTTTGG
ttttgat putative branch site (score: 4)
ttcttgttc putative PPT
aagtaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttgtcacatctgagggagatcagttagtaacagttggattttgattcaagtaaaaccgctcattctggtcacatctgaacgttcttgttcatcgcagGTAGTGATGCCTACAGTGGAAGCTGATGTGGCATTTGGTCTTGGCAAGTATCATGACATGAATCAGGAAGAAGTTAAGTCTAGGGTGATTAAAGCTTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - tcacatc
- - - - - - - - - - - - - - agtaaca
- - - - - - - - - - - - - - - - - - - -gattttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -taaaacc