Sequence
atgc intronic sequence ATGC exonic sequencegtgagttatatttaacagctcatcagttacttaaacactttttgggacaagcagttcaaactcatgttccaatcctaaaattaattgcaattcacagGGAAGAAATGCAGATTCTTTATCTCACTACTTCGGTGAGGATCCAGCTCGATGTCCTTTTGAGCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G31810.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os10g02980.1 (Oryza sativa), 3'ss of exon 12
gtgagttatatttaacagctcatcagttacttaaacactttttgggacaa-gcagttcaaactcatgttccaatcctaaaattaattgcaattcacagGGAAGAAATGCAGATTCTTTATCTCACTACTTCGGTGAGGATCCAGCTCGATGTCCTTTTGAGCAAG
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---------------------gtgagtccctactgtatttttttttacaaagttatttgtgtt--tggaaagatcctgacaacattaat--tttgtagGGAAGAAACGCTGATTCACTAGCTCAGTATTTTGGCGAGGATCCAGCACGATGCCCTTTTGAGCAAG
upper sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA04G14770.1 (Glycine max), 3'ss of exon 16
----------------------------------------------------------------------------------gtgagttatatttaacagctca--------tcagttacttaaacactttttgggacaagcagttcaaact---catgttccaatcctaaaattaattgcaa--ttcacagGGAAGAAATGCAGATTCTTTATCTCACTACTTCGGTGAGGATCCAGCTCGATGTCCTTTTGAGCAAG
| || || || | || | || ||| | || || | || || | | | |||| || || | | || ||| || |||||||||| |||||| ||||| || || ||||| || |||||||||||| |||| |||||||| ||||
gtgagtcctgttaaagttatatttcctctcttcctcctttttccttggtgttgctcttgacttgtagattgcctgctcagaggagaatttgatgcaccatcccagataatagtcactagtttggactatgttgataactaagtctgccaactacgtattttttggttttggtcttgattctttcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGGGAGGATCCAGCTAGATGCCCTTTTGAACAAG
upper sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA09G34830.1 (Glycine max), 3'ss of exon 16
----------------------------------------------------------------------------------gtgagttatatttaacagctca--------tcagttacttaaacactttttgggac-aagcagttcaa--actcatgttccaatcctaaaattaattgcaa--ttcacagGGAAGAAATGCAGATTCTTTATCTCACTACTTCGGTGAGGATCCAGCTCGATGTCCTTTTGAGCAAG
| || || || | | | || ||| | || || | || || ||| ||| ||| || || | | || ||| || |||||||||| |||||| ||||| || || ||||| || |||||||||||| |||| |||||||| ||||
gtgagtcctgttaaagttatatttcatctcttcctcctttttccttggtgttgctattgacttgtattttgcctgctcagaggagaatttgatgcaccgtcccagataatagtcattagtttggactatgttgataaccaagtctgccaactacttattttttggttttggtcttgattctttcttttccagGGAAGAAGTGCAGACTCTTTGTCCCAGTACTTTGGAGAGGATCCAGCTAGATGCCCTTTTGAACAAG
upper sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 16
gtgagttatatttaacagctcatcagttacttaaacactttttgggacaagcagttcaaactcatgttccaatcctaaaattaattgcaattcacagGGAAGAAATGCAGATTCTTTATCTCACTACTTCGGTGAGGATCCAGCTCGATGTCCTTTTGAGCAAG
|||||| | | | || | ||| || ||| | | | | | ||||| | || | || | |||| | ||||||||||||||||| || || || || ||||| || || ||||||||||| ||||| ||||||||||
gtgagtcttctccatggtctta---gttgct--gacaactgt--gagtatgtagttcgg-tactgattttggtactgctac--attgt--cttgcagGGAAGAAATGCAGACTCCTTGTCCCAGTACTTTGGAGAAGATCCAGCTCGGTGTCCATTTGAGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggacaagcagttcaaactcatgttccaatcctaaaattaattgcaattcacagGGAAGAAATGCAGATTCTTTATCTCACTACTTCGGTGAGGATCCAGCTCGATGTCCTTTTGAGCAAG
taaaattaattgcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttatatttaacagctcatcagttacttaaacactttttgggacaagcagttcaaactcatgttccaatcctaaaattaattgcaattcacagGGAAGAAATGCAGATTCTTTATCTCACTACTTCGGTGAGGATCCAGCTCGATGTCCTTTTGAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG