Sequence
atgc intronic sequence ATGC exonic sequencegtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19160.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os08g12890.1 (Oryza sativa), 3'ss of exon 8
gtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttct-ttatccataatatac-ttatggtctgataaatttcg--cagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC
||| | ||| | | || | || || ||| | || | || ||||| || |||| | || ||||| | |||||| | || ||| |||| |||||||| ||| ||||||| |||||||||||||||||| ||||||||||||| || | | || | ||| | ||
-------gtcagt--agttcagtatacaatgcccattctta---tttgaaaacctactattatcaatcatatctgctgaattcgtttaaatgccaaccagATGATGGACCCTGCTGGAATTGCTAATTGGTCTGTGACTTATGTTGATTGGTCTGAGGGAAAGTGGCATCCCAGGTCTTTCCGAGCTAAGGATGTAACTT
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
gtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC-
| | ||| || | ||||| | ||||| ||| | | | ||| | | | | | | || ||||||| ||||||| ||||| ||||| || ||| | |||||| |||||||||||||||| |||| |||||||| | | |||| | ||| || | || ||
----------gtaagaactctcaaaaactcttaaatgat--gtttttcagttgtgtttacttcc-cagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACA-CAAGCT
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g45110.1 (Oryza sativa), 3'ss of exon 8
gtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC
|| || ||| |||| | | || || | ||||||| ||| | | || | |||| ||| | | | || | |||||| | |||||| ||| |||||||| ||| | || ||| ||||||||||||||||| |||| |||||||| || ||| | ||| |||| ||||
gtcagtatttatttacaatatattgaagtg----acatttgattcttttgggggct---tacttgctaaatacatatcattttgcatatctt-cagATGGTAGATCCTGGTGGAATTGCTAATTGGTCAGTTACACATGTTGATTGGTCTGAGGGAAAATGGCATCCGAGGTCATATAGAGCTGCAGATGTCACCT
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
gtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC
|| || | | | ||| | || || | | || || || || | || || || | |||| ||| | | || |||||| | |||||| ||| || |||| ||| | |||||| |||||||||||||||| |||| ||||||||||| || | || ||| | ||
gtcagtaaataat---attttgaattgatatttagctttc---ttcttggtcccttgcttttctttcatatgctttcactttcat-----cttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
gtgag-aattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC
|| || |||| |||| | ||| | | | ||| || | ||| | | | || || | ||| ||||| |||| ||| ||| || ||||||||| | ||||| ||||||||||||| ||| |||| ||||||||||| ||| | ||| |||| | ||
gttagtaattatttttaactctgtt--------atttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
gtgag-aattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC
|| || ||| | ||| | | | | | || | | | | | |||||||| | | |||| ||||| | |||| |||||| | |||||| ||| || ||||||||| | ||||| ||||||||||||| ||| |||| ||||||||||| ||| | ||| |||| | ||
gttagtaatccttttcaactgttatttgcctttaatttcctcgatccct--tgctttcttttttaa--gtatagttatgttttgat-----cttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
upper sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G06790.4 (Glycine max), 3'ss of exon 7
gtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC
||||||||| ||||||| | || ||| ||| | ||| | | || | | || ||| | | | | | ||||| |||||||| ||||||||| |||||| | | || |||||||||||||||||||||| ||||| || | | ||||| | || | ||| | ||
gtgagaatttg----aattctaat----------acagttcttttgttaacatttt--tcagcctttagctaatta-gcttttgtctctgatttagATGGTTGATCCTGGTGGCATTGCAAACTGGTCACTAACTCATGTTGATTGGTCTGAGAGAAAATGGCACCCTAAATCATACAGGGCTCAGGATGTTACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC
gtctgat putative branch site (score: 4)
tttatccataatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA