Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttcttctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G25800.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttcttctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
||| || | | | | | | | | | || | | || | || ||| |||| || ||| | || ||||||| |||||||| || |||||||| ||||| |||||||| ||||||||||| ||||| || || ||||| | || |||||||| || | | || ||
gtaagt-----cctctgaagcaaccatgatatgatacgattcttcatgatatttct----attaac-tgtt--tgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttct-tctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
| | | | | | || ||| | ||||||| | | |||||| | || ||| | | | |||||||||||||||| ||||||||| | |||| |||||||| |||||||| || || || || || |||||| | || ||||||||||| | | | ||
-------gtaagtcccaaaaatgtatctgtgtactgtattc-ccacttgacatatatctaaactat-------ttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G010471_T01 (Zea mays), 3'ss of exon 1
gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttct-tctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
| | | | ||| || ||| | |||||| | | |||||| | || ||| | | | |||||||||||||||| ||||||||| | |||| |||||||| |||||||| || || || || || |||||| | || ||||||||||| | | | ||
-------gtaagtcccaaaaatgtatttgtgtgctgtattc-tcacttgacatatatctaaactat-------ttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 4
gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttcttctaa-atcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
|| | || ||| ||| | | ||| | | || | | ||| || || || | ||| | | || ||||||||| |||||||||||||| ||||| | || |||||||| ||||| ||||| |||||||| || ||||| | || || ||||| ||| | | ||
----gtatgtttatttagtgtgatgtcattgttaaataatc-taacatataggctttaaacatgaatacgttaactaactcttt---tgtagTGTATAAGAAGCATTATCCTCCTGCACTAAAGGATGAGGTATGGAGATTAGAAAAGATTGGAAAGGATGGTTCATTCCACAAGAGATTAAACTCAAGTGG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 5
gtatgtgttttcttttcttg-ttctctttttgccttgtgcttg--ccacttgttttcttctaa-----atcaacatgt-tgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
|||||||| | ||| || || || | | || ||| || || || ||| || | || || || || | |||||||||||||||| || |||||||| |||| ||||| || ||||| ||||| |||||||| || ||||| || || || |||| | ||| || ||
gtatgtgtgacacactgttgatttactcattagatgaaacaaagattacctgtatttttagaatttgcatcgccaagcatgctgattttgtatttattagTGTACAAGAAGCACTACCCACCTGCGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCCAGTGG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 6
------gtatgtgttttcttttcttgttctctttttgcctt--gtgcttgccacttgttttcttctaaatcaacatgttgttggattggttatgtg----------tagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
|||| | | | | | || | | | | | | | ||||| || || | | || | | ||| || | || | | || ||| || |||||||||||||||||||| |||| |||||| |||||||| || |||||||| || || |||||| | |||||||||| ||| | ||||||
gtagggttatgcttctacatcttttagtttttctctagcatcagtgctctcc-ctgctcctacactgtaatagcatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCTGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTTCATAAGAAGCTGAATAGTGCAGG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
------gtatgtgttttc-ttttcttgttctctttttgcct---tgtgcttgccacttgttttcttctaaatcaacatgt---tgttggattg----gttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
|||| | | | | || | ||| | | | || | | || | | | | ||| | | || | | | | || ||| || | ||| || ||||||||||||||||| || |||| |||||| |||||||| || |||||||| || || |||||| | || ||||||| ||| | ||||||
gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
----gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttctt--ctaaatcaacatgttgttggattggttatgt--------gtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
|| | | || | || || ||| || | || | ||||||| || ||||||| ||| || | | | | |||||||| ||||| || ||||||||||| || | |||||| |||||||| || ||||||||||| || ||||| | || || |||||||||| | |
gtaggttcaggctcatccttgtcttttatttattgaattat-tttattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgtt----------------ttcttctaaatcaacatgttg-------ttggattgg---ttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCT-AACCGCTGCAGG
| | ||| | | || || || | || | | || | | || || | || |||| || | | ||| | |||| || ||| ||||||||||||||| ||||||||||| |||||||| ||||| ||| | || || |||||||| || || || || ||||| ||| | || || | |
gtacgttgactgttttgaaccttgggtcatcttacgctataagagtttgtctgcgttcctaatttacagttagtttcgttttaggcagttaataaaagcagtttgaatatttatctagatggaagtattgaatcttttctacttgggaatttcgtgcagTGTACAAGAAGCACTATCCACCTGCCTTGAATGACGAGGTATGGCGCTTGGACAAGATTGGGAAGGACGGAGCCTTTCACAAGCGCCTCAATCAAAACCA-
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S98_167V6.1 (Physcomitrella patens), 3'ss of exon 4
----gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttg------ttttcttctaaatcaacatgttgttggattggtta---tgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
| || | | || || | || |||| ||| || || | | |||| ||| | |||||| ||||| | ||| ||| ||||||||||| ||||| |||||||| ||||| ||||| ||| | || || |||||||| ||||| || || || || || | |||| ||| |
tgccctgtgcacatccattcgttctgtgctgaatgcc--gtgattaacagaagaaaaatcatatctctatatctaataattgttg--ttggtcaccttgtacagTCTACAAGAAGCACTATCCGCCTGCTTTAAATGACGAGGTTTGGCGATTGGACAAGATTGGAAAAGACGGTGCTTTCCACAAACGTCTAAATCAAGCAAG
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S34_132V6.1 (Physcomitrella patens), 3'ss of exon 4
----------gtatgtgttttcttttcttgttctctttttgccttgtgcttgcc--acttgttt-tcttctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
| ||| | | | | | ||| ||| || | | | | || | || | |||||||| | | ||| ||| ||||||||||| |||||||| || |||||||| ||||| ||| | || || |||||||| ||||| || || || || ||| | |||| ||
tctgccagatttccaagttgtgatcagaagaagaaagaagggatggtgaaagcccaacatatctgtatttttgattat--tgttgttgatt--actctgttcagTTTACAAGAAGCACTATCCACCAGCCTTGAATGACGAGGTTTGGCGATTGGACAAGATTGGGAAAGACGGTGCTTTCCACAAGCGTCTAAATCAAGCTCA
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttcttctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCT-AACCGCTGCAGG
||| || | |||| ||||||| | || || || || | | | | || || | | |||| ||||||||||||||||||||||||||| || | || ||||||||| | | || ||||| || || || ||||| || || ||| |||| || | | |
gtaagttggcgactgaactgtt-tcttttttttgtttggttttgacatgctgcttaccgatgttacgtgc---------gctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG-
upper sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ11323 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttcttctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCT-AACCGCTGCAGG
||| || || |||| ||||||| | || || || || | | | | || || | | |||| ||||||||||||||||||||||||||| || | || ||||||||| | | || ||||| || || || ||||| || || ||| |||| || | | |
gtaagttggccacttaactgtt-tcttttttttgtttggttttgacatgctgcttaccgatgttacgtgc---------gctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttgccacttgttttcttctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
ttctaaa putative branch site (score: 2)
ttctaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttcttctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG