Sequence
atgc intronic sequence ATGC exonic sequencegttctttacctttttactttggtaaatttagaccaataaattactcattcttatgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G37180.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G37180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G04990.1 (Glycine max), 3'ss of exon 9
-----------gttctttacctttttac-tttggtaaattta--gaccaataaattactcattctta-tgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
|| || | |||| || |||| ||| | | | || | || || || ||| |||| || | ||| | ||| |||||| |||||||| || ||||||||||| ||||||||||||||| |||||||||||||||| ||||| || ||||| ||||||| |||||| | ||
gttactaccctattattgaaattttcctattcagtaacttttgtggctgtaaggatatccttttttgctgcataaattaattccccaggttgcttggaaa-----ccagGGAACTATCGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAGTTAGATCCCAAGTATCACTTCTCATGTCAATTCATGG
upper sequence: AT5G37180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G33240.1 (Glycine max), 3'ss of exon 8
gttctttacctttttactttggtaaatttagaccaataaattactcattcttatgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
|| | | || || | | | ||| |||| | || | ||| | ||| |||| |||||||||| || ||||||||||| ||||||||||||||| ||||||||||||| || ||||| || ||||| ||||| | |||||| | ||
--------------------------------gtaaggatgtccttgttgctgtat--aaattaattcctcaggttgcttggaaa-----ccagGGAACTGTTGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAATTAGATCCCAAGTATCACTTCTCTTGTCAATTCATGG
upper sequence: AT5G37180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 9
-----------gttctttacctttttactttgg-taaatttagaccaataaat-tactcattcttatgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
|| |||| |||| || | ||| | || | || | || || | | | ||| | | || ||| | ||| |||||| |||||||| || |||||||| || |||||||| |||||| |||||||||||||||| || || || || || ||||| | |||||| | ||
gtcactataagtttttttaagttttcctttcaactgtttttgtggctgcaagtatatgtgtgtttttgct-acgtgtactaattcca-tatggtaatttaaaaccagGGAACTATAGCACATGCTTTAGAGAAGACCAAGTATGAAGACTCAGATGTCAAGTGGAAAGAGTTGGACCCCAAGTACCACTTCTCGTGTCAATTCATGG
upper sequence: AT5G37180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G40740.1 (Glycine max), 3'ss of exon 8
-----------gttctttacctttttactttgg-taaatttagaccaataaattactcattcttatgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
|| |||| |||| || | ||| | || | | | || | | | | | ||| | | || |||| | ||| |||||| |||||||| || |||||||| || |||||||| |||||| |||||||||||||||| || || || || || ||||| | |||||| | ||
gtcgctataactttgtttaagttttcctttcaactgtttttgtggctgcaagtatatgtcttttttcgctacgtgtactgattccatagcttgattgaaaacc-agGGAACTATAGCACATGCTTTAGAGAAGACCAAGTATGAAGACTCAGATGTCAAGTGGAAAGAGTTGGACCCCAAGTACCACTTCTCGTGTCAATTCATGG
upper sequence: AT5G37180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv04s0079g00230.t01 (Vitis vinifera), 3'ss of exon 8
gttctttacctttttactttggtaaatttagaccaataaattactcattcttatgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
|| ||| || ||| | |||| || | | || || | | | | | | | | ||| | | | ||| || ||||| |||||||||||||||||| ||||||||||| || |||||||| ||| |||| ||||| || || || || |||||||||||||||| |||||||| |
gtgtttttactcattagt--ggtagatagtttgctactaaatataaactgtcttcttgctagctacttactaatctaaaatgccctgaaactagGGAACTATTGCACATGCCTTAGAGAAGACTAAGTACGAAGATTCGGATGTCAAATGGAAGGAATTAGAGCCCAAATATCATTTCTCATGCCAATTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attactcattcttatgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
aaacaaatttattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctttacctttttactttggtaaatttagaccaataaattactcattcttatgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA