Sequence
atgc intronic sequence ATGC exonic sequencegtaattctcataagtctatctcgtcttcttttatctatgattcaatcattttcacttccttactgactaatttcatctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCACAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G32880.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC187157.4_FGT005 (Zea mays), 3'ss of exon 4
-------------------------------------------------------gtaattctcataagtctatctcgtcttcttttatcta-tgattcaatcattttcacttccttactgactaattt-------catctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCACAAGG
| | | | ||| || |||| || | | || ||| || | | | | |||| | | | | ||||||||||||||||||| || |||||| |||| || || ||||| ||| | || |||| || || ||||||||||| ||||| | || || | |
gttggtcacggcctctgaatcactactactatttcgcttgcttgtttgcctctgaatcactattatattccttcctcgcgcggcttaactgaactgctccatcgttcttgcctacgtactctccattccatgggcacccttgcagCCTGGTCCGGATTCTATTGGAATCATTGCCATCTCGCATGGCTGCCCCGGTGTCGCCGCGCGAGCTTGCGGCCTCGTGGGCATGGAGCCTGCGAAA
upper sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G09100.1 (Glycine max), 3'ss of exon 4
-------------------gtaattc--tcataagtctatctcgtcttcttttatctatgattcaatcattttcacttccttactgactaatttcatctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCACAAGG
|| || ||| | | | | || |||| | || ||| | ||| || || | | | || ||||||||||||||||||| |||||||||||||||||||| || ||| | ||| | ||||| ||||||||||||||||||||||| || || || |||
tgttgtctagtactatttaatactttggccatgcacttgttttttttttttttgttaattgcgtaat-gtaaatactaatttttgttctgaat--gtttgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCTGCACGTGCTTGCGGCCTTGTGGGTCTAGAACCTACCAGG
upper sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G09000.1 (Glycine max), 3'ss of exon 1
-------------------gtaattctcataagtctatctcgtcttcttttatctatgattcaatcattttcacttccttactgactaatttcatctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCACAAGG
|||| || | | | || |||| | | ||| | || | | | | | | | || ||||||||||||||||||| |||||||||||||||||||| || ||| | ||| | || || ||||| ||||||||||| ||||| || || | |||
ttctagtgttgtgtactatttaatactt-tggccatgcacaatttttttttttggttaattgtgtaatgtaaatattaatttttgttctgaatgtttgtagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCACGGTTGCCCTGGAGTGGCCGCACGTGCCTGCGGCCTTGTTGGTCTAGAACCTGCCAGG
upper sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g03250.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtaattctcata-agtctatctcgtcttctttta--tctatgattcaatcattttcac----ttccttactgactaatttcatctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCACAAGG
|| | | || | | | | | | || || || | | ||| | | || ||| | | | |||||||||||||||||||||| ||||||||||||||||||||||| ||||| ||| | || || || || ||||||||||| |||| || || |||||
tgggtgacattgtggctttgctacaatatcttctgaccaaaactagtcctgtgttcctgctcctttttcgtaatctctatttgatctgtcccctgtgcagCCTGGTCCGGATTCCATTGGAATCGTTGCTATTTCTCATGGTTGCACTGGAGTGGCAGCACGCGCATGCGGCCTTGTCAGTCTAGAGCCAACAAGA
upper sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S67_107V6.1 (Physcomitrella patens), 3'ss of exon 7
------------gtaattctcataagtctatctcgtcttcttttatctatgattcaatcattttcacttc---cttactgact-----aatttcatctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCA-CAAGG---
| | | | | | | | | ||| | | || || | | | | || | | | || | || | ||||||||||||||||| |||| || || |||||||||| || || ||| ||||| |||||||| || ||||||||||||| || ||| | || |
ttatctcaagttctgaatttggtga--cgaattgaaattcacagaagtggaatacatacgtcattatttagaacaaattaacggtgagatgtttttgtgcagCCTGGTCCGGATGCCATTGGCATTATTGCTATTTCCCACGGTTGCGTTGGAATAGCTGCTCGAGCGTGCGGCCTTGTGGCCCTCGATGCTGGTAAAGTTA
upper sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S55_99V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------gtaattct-cataagtctatctcgtcttcttt-tatctatgattca-atcattttcacttccttactgactaatt-----tcatctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCA-CAAGG---
| || | || | | || | ||| || || | | | | | | || ||| || | | | ||| ||||||||||||||| |||| || ||| ||||||| || || || ||| ||||| |||||||| ||||||||||| |||| || ||| | | ||||
gtatgaaatttcttcgagatggtcttcacttcgcggactgagtatggtgactacttgtggagtgaatcacctcttacacacctatccaatgatgttgtattacccaatgtgatctcaaaaacgtcaattacatgcagcgctattaagctctaactaacgagctggtgttgctctccagCCTGGTCCGGATGCCATTGGCATCATTGCTATATCCCACGGTTGCGTTGGAATAGCTGCTCGAGCTTGCGGCCTAGTGGCCCTCGATGCTAGTAAGGTTA
upper sequence: AT4G32880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S15_11V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaatt------ctcataagtctatctcgtc--ttcttttatcta---tgattcaatcattttcacttcc--ttactgactaatttcatctgca-----gCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCA-CAAGG---
||||| || | ||| || | |||||| || | | | | || || | | || |||| | | |||| ||||||||||||| |||| || ||| ||||||| || ||||| ||| ||| || || ||||| || |||||||||| || || ||| | ||| |
ttaatttaggagctaacaaggtaatgatattgattctttaattcaaattaaagtggttgattgcaaatgccattgctgatacgtcactagtgcaatgcagCCTGGTCCGGATGCCATTGGCATCATTGCTATATCCCATGGTTGCGTGGGCATAGCAGCTCGAGCGTGCGGCCTTGCGGCGCTCGATTTTAGCAAAGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttatctatgattcaatcattttcacttccttactgactaatttcatctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCACAAGG
tttcatct CT-rich tract
aatcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattctcataagtctatctcgtcttcttttatctatgattcaatcattttcacttccttactgactaatttcatctgcagCCTGGTCCGGATTCCATAGGAATCGTTGCTATTTCTCATGGATGCACGGGAATCGCTGCTCGTGCTTGCGGCCTTGTGGGTCTTGATCCCACAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT