Sequence
atgc intronic sequence ATGC exonic sequencegtacaattgttttactcaatgagcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagttttgacttgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39590.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
gtacaattgttttactcaatgagcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagttttgacttgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG
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--------------------------------------------------------------------gttagccctcctc------aaccttatgcc-catttgaattgcttcattctgaggatacgcccctgattattattgttctatat-tagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G328578_T01 (Zea mays), 3'ss of exon 2
gtacaattgttttactcaatgagcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagttttgacttgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG
||| || || ||| || || | | || || | || ||| | | | || | || | | |||| |||||| ||||| || || |||||||| |||||| | |||||||| ||||| ||||| |||||||| || || || || ||||||||||| || ||
--------------------------------------------------------------------gttagccctcctc------aaccttatgcc-catttgaattgcttcattctgaggatacgtccctgattattattgttctatat-tagGCTACATTAGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G083497_T04 (Zea mays), 3'ss of exon 1
gtacaattgttttactcaatgagcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagttttgacttgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG
| | | || | | | ||| ||| || || || || || | || | | | |||| ||||||| ||||| || || |||||||| |||||| | |||||||||||||| || || || || || || ||||| |||||||| ||||| || ||
------------------------------------------------------------------------------gttagttctcaatctcgtgccccatttcaattggcagcattccgaggatacgtacctgattagtgctatattat-tagGATACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATTGTGGTGGAACTGAACGGCAGACTAAACAAATGCGGTGTAATTAGCCCCCG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g00530.t01 (Vitis vinifera), 3'ss of exon 3
gtac-aattgttttactcaatgagcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagttttgact-tgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG
|||| ||| || | | ||| ||| |||||| | || ||| || || ||| || || | || | || || | || ||| || |||| | | || | |||| |||| | || ||||||||||| ||||||||| ||||| ||||||||||| || || |||||||| ||||| || |||||||| || ||||| || || ||||| ||||| ||
gtactaatcaattcatt---tgaatttcagattgtttcaattttcttttcttcttt---actt-------ttgcattgttttt---------ttttgttacct-----gtgtacatttttattcacgtattttactga--ttttattttgctctacagGTTACATTGGAGAGTTTGAGTATGTTGATGATCACAGGTCTGGAAAGATTGTTGTTGAACTGAATGGAAGACTAAACAAATGTGGGGTTATCAGTCCCCG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 2
gtacaattgttttactcaatg-agcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagt-tttgacttgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG
||| | ||| ||| || || || ||| || ||| ||| | || | || | || |||| | || || ||| | ||| | | | ||||| || | ||| | | | ||||||| | ||| || || | || ||||| ||||| |||||||||||||| || || |||||||||||||| ||||||||| | ||||| || ||||| |||||||||||
----------gttagtgcatgtagcacctattttatttattctcttcgatttctttcgtttctactg---ttttgatgtgtcgattcaagtatgagtgaaaattaataatttatattgtttgatgtgtca-acatca-tctctgcctttggcctgcagGATATATCGGTGAATTTGAGTATGTAGATGATCACAGATCAGGAAAAATTGTGGTTGAGCTGAATGGAAGGTTGAACAAGTGTGGTGTCATTAGTCCTCG
upper sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S426_18V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacaattgttttactcaatgagcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagttttgacttgaaacacacaaactttttcctttgg---tttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG
|||||| | | | | | || | ||| || | || | | ||| || | ||| |||| | | | | || ||||| ||| |||||| |||| ||||||||| ||| ||||| ||| || | || ||||||||||| ||||| |||||||| | ||||| |||||||| || ||||||||
-----------------------------------------ctctctctctctctctcatctacgaaaat-----------aaactatttatcttcgcgtct----aagttgcagcattgatagcggat---cgttttctctcttttggctcttttcagGTTATATTGGAGAGTTTGAGCTTGTTGATGACCACCGAGCTGGCAAGATTGTGGTAGAGCTCAATGGAAGATTGAACAAGTGCGGTGTCATCAGTCCTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcaaatgttcagttttgacttgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG
ttttgac putative branch site (score: 3)
ctttttcctttggttt putative PPT
aaacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaattgttttactcaatgagcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagttttgacttgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG