Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaaatcagccaccaagactgactttcacttttttcattagatatacatttgtttgttccaaatgtttcctttacgttgtccaattgaaacagGTAAAGGTCTTTGGGTCCATCGCTTATGTTTCTCAGACTTCTTGGATCCAAAGTGGTACCATCCGGGACAATATCCTCTATGGAAAGCCCATGGAAAGTA
Basic information
| species | Arabidopsis thaliana |
| transcript | AT3G21250.2 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G20780.1 (Glycine max), 3'ss of exon 3
---------------------gtaagcaaatca-gccaccaagactgac---tttcacttttttcattagatatacatttgtttgttccaaatgtttcctttacgttgtccaattg--aaacagGTAAAGGTCTTTGGGTCCATCGCTTATGTTTCTCAGACTTCTTGGATCCAAAGTGGTACCATCCGGGACAATATCCTCTATGGAAAGCCCATGGAAAGTA
| || | || | || || ||| | | | ||| | | ||| | | ||| || | || || |||| || || |||||||| | || | ||| | | || || ||||| || ||| ||||||||||||||||||| || || || ||||| ||||||||||| || ||||| |
gtgagttattgatcatccaaatttagtatattataacattaaacatgaagcaacttagtaattttaatgactattaaactctttatttatttttcttttttgctcttgtgaaaatggaaaacagGTTAGTGTATGTGGAACACTTGCCTACGTTTCCCAAACTCCTTGGATCCAAAGTGGTACAATTCGTGATAATATTCTCTATGGAAAACCAATGGATGAAA
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G20360.1 (Glycine max), 3'ss of exon 1
gtaagcaaatcagccaccaagactgactttcacttttttcat-tagatatacatttgtttgttccaaatgtttcctttacgttgtccaattgaaacagGTAAAGGTCTTTGGGTCCATCGCTTATGTTTCTCAGACTTCTTGGATCCAAAGTGGTACCATCCGGGACAATATCCTCTATGGAAAGCCCATGGAAAGTA
|| || | | | | |||| | ||| | | || | |||| || | ||||| | || |||| | | || |||||||| || || ||| | || || ||||||||||| ||||||||||| |||||||| || | ||||| ||||| |||| |||||||| ||||| | |
gtgagttattaaccatacaagtttagttttttgtcatgccaaattcatatttatatttttgtccttgatatttcatgataatggt-------aaacagGTGAATGTAGGTGGCACAATAGCCTATGTTTCTCAAACTTCTTGGATACAAAGTGGGACAGTTCGGGATAATATACTCTTCGGAAAGCCAATGGACAAAA
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G01390.1 (Glycine max), 3'ss of exon 1
gtaagcaaatcagccaccaagactgactttcacttttttca---ttagatatacatttgtt-tgttccaaatgttt----cctttacgttgtccaattg----aaacagGTAAAGGTCTTTGGGTCCATCGCTTATGTTTCTCAGACTTCTTGGATCCAAAGTGGTACCATCCGGGACAATATCCTCTATGGAAAGCCCATGGAAAGTA
|| || | | | | | |||| | ||| | | ||| | | | || | | || ||| | | ||| || | | || | |||| |||||||| || || | ||| | | || ||||||||||| ||||||||||| |||||||| || | || || ||||| |||| ||||||||| ||||| | |
gtgagttattaaccaaacaagtttagttttttgtcatgtcaaattcatgtttataatccttgtgtctaacacttttttgtccctgaaattttacaataactgaaaacagGTTAATGTGTCTGGCACTGTAGCCTATGTTTCTCAAACTTCTTGGATACAAAGTGGGACAGTTCGAGATAATATACTCTTTGGAAAGCCAATGGACAAAA
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 13
gtaagcaaatcagccaccaagactgactttcacttttttcattagatatacatttgtttgttccaaatgtttcctttacgttgtccaattg-aaacagGTAAAGGTCTTTGGGTCCATCGCTTATGTTTCTCAGACTTCTTGGATCCAAAGTGGTACCATCCGGGACAATATCCTCTATGGAAAGCCCATGGAAAGTA
| || | || || ||| | | || | || | ||||| || | | ||| ||| || | | | ||| |||||||| | || ||||| ||||| || ||||||||||| |||||||||||||||||||| || || || ||||| || ||||| ||||| || ||||| | |
--------gtgagttgc-aaaacca--tttagtatcatagatcatttacaaatttgatt--tgctaatttttttttcccttctgctggttgcaaacagGTTGATGTATTTGGTTCCATTGCCTATGTTTCTCAAACTTCTTGGATCCAAAGTGGGACGATTCGTGACAACATTCTCTACGGAAAACCAATGGATACAA
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g02430.t01 (Vitis vinifera), 3'ss of exon 2
gtaagcaaatcagccaccaagactgactttcacttttttcattagatatacatttgtttgttccaaatgtttcctttacgttgtccaattgaaacagGTAAAGGTCTTTGGGTCCATCGCTTATGTTTCTCAGACTTCTTGGATCCAAAGTGGTACCATCCGGGACAATATCCTCTATGGAAAGCCCATGGAAAGTA
| || | || | ||| || | || | || | |||||||| | | | |||||| || | || |||||||| | || || || ||||| || |||||||||||||||||||||||||||||||| || || || ||||| || |||| |||||| || ||||| | |
--------gtgagttgcaaaatca---tttagtgttatagatcatttacaaatttgttt-tactacatgtttttcttctgatggttgc---aaacagGTCGATGTGTTCGGTTCCATTGCCTATGTTTCTCAGACTTCTTGGATCCAAAGTGGGACGATTCGCGACAACATTCTCTGTGGAAAACCAATGGATACAA
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g02440.t01 (Vitis vinifera), 3'ss of exon 1
gtaagcaaatcagccaccaagactgactttcacttttttcattagatatacatttgtttgttccaaatgtttcctttacgttgtccaattgaaacagGTAAAGGTCTTTGGGTCCATCGCTTATGTTTCTCAGACTTCTTGGATCCAAAGTGGTACCATCCGGGACAATATCCTCTATGGAAAGCCCATGGAAAGTA
| || | ||| | |||| || || || | || | |||||||| | |||| ||| | || |||| ||||||| | || ||||| || ||||| ||||||||||| |||||||||||||||||||| || || || ||||| || || ||||||| ||| ||||| | |
--------gtgagttgcaaagcc---ctttagtattattgatcatctacaaatttgttt-cactaaattttttccttctgttggttgtc---aacagGTTGATGTATTTGGTTCAATCGCCTATGTTTCTCAAACTTCTTGGATCCAAAGTGGGACAATTCGCGACAACATTCTTTATGGAAGGCCAATGGATAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagatatacatttgtttgttccaaatgtttcctttacgttgtccaattgaaacagGTAAAGGTCTTTGGGTCCATCGCTTATGTTTCTCAGACTTCTTGGATCCAAAGTGGTACCATCCGGGACAATATCCTCTATGGAAAGCCCATGGAAAGTA
atacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaaatcagccaccaagactgactttcacttttttcattagatatacatttgtttgttccaaatgtttcctttacgttgtccaattgaaacagGTAAAGGTCTTTGGGTCCATCGCTTATGTTTCTCAGACTTCTTGGATCCAAAGTGGTACCATCCGGGACAATATCCTCTATGGAAAGCCCATGGAAAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
