Sequence
atgc intronic sequence ATGC exonic sequence...tgtttggtttggtttcctttttctgccatcatcttgtttagaatgcaattatcaatcaactcactgactggtactatctacttgtgatgacttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02840.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 3'ss of exon 2
tgtttggtttggtttcctttttctgccatcatcttgtttagaat-gcaattatcaatcaactcactg------actggtactatctacttgtgatgact-taatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA
| | | |||| || || || ||| | || | | | || | | | || ||| | | | || | || |||||| ||| | ||||||||||| || | ||| ||||||||||||| |||||||||| ||||| ||||| || || ||| | ||||| |||||||||||
--------tcagcagagctattctcatgcggtcatgcctataatcacctccataagtgactccattatactccatatgcacatcctaacttccaggtctattttgtagGTGTTGATATCAGCATGAACACGCACCTGAAAACTGTGAAACTCACATTGAAAGGGAAAAATCCTGTTACCTTTGATCACCTCAGTGTGAGGGGAAACAA
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 3
tgtttggtttggtttcctttttctgccatcatcttgtttagaatgcaattatcaatcaactcactgactggtactatctacttg-tgat-----gactt--aatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA
| || | ||||||| || | | | | | ||| || | | | | ||||| || || | | | ||| |||| ||||| ||||||| ||| | || |||||||| ||||| ||| | || ||||| |||||||||||||| |||||||| || |||| || | ||||| ||||| |||||
----tagtcag---tccttttactatcttgcttctttctagt-tgaactacaccagcaactttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA
upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 3
tgtttggtttggtttcctttttctgccatca--tcttgtttagaatgcaattatcaatc-aactcactgactggta--ctatctacttgtgatgacttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA-
| || ||| | | || | || | | || | | | || || | | || || | | | || ||||||| ||| | || |||||||| ||||| ||| | || ||||| |||||||||||||| |||||||| || | || || | ||||| ||||| |||||
------agtgagtcctcttactatattgctgcttcctagttgaactacaccaacaactttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caattatcaatcaactcactgactggtactatctacttgtgatgacttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA
acttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttggtttggtttcctttttctgccatcatcttgtttagaatgcaattatcaatcaactcactgactggtactatctacttgtgatgacttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA