Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcttcttctttccttaatagggtcgaatttgttttaaagcagtttcttaaacaaatttttgtttctgtcagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22120.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------------------------------------gtaagtttcttcttctttccttaatagggtcgaatttgttttaaagcagtttcttaaacaaatttttgtttctgtcagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC
|| ||| | || || | ||| | || | | ||| | |||| ||| || | | |||||| || || || || |||||||||||||||||||| ||||| ||||||||| ||||||||||| | || |||| ||| | |||||||| ||||||
gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgca-taacttacacag---cttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
upper sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 10
--------------------------gtaagtttcttcttctttccttaatagggtcgaatttgttttaaagcagtttcttaaacaaatttttgtttctgtcagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC
|| ||| | || || | ||| | || | | ||| | |||| ||| || | | |||||| || || || || |||||||||||||||||||| ||||| ||||||||| ||||||||||| | || |||| ||| | |||||||| ||||||
aactaaaacgaaacagaggagtattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgca-taacttacacag---cttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
upper sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G16230.3 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------------------------------------gtaagtt--tcttcttctttccttaatagggtcg-aatttgt---tttaaagcagtttcttaaacaaatttttgtttctgt----cagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC
|| || || | | | ||| | || | ||| | | | | || || | | | |||||| ||||||||||||||||| ||||| || || ||||||| |||||| || ||||| || || ||| || || | ||| || | | |||||| | ||
gtcatcaggtacagagatgttaaatttatatatgcacgtttacgattctggtgccattaatcattcattaaaaaatgcacacaacacagttaacaccataatggcttatacattaatccctattatacattagcaccgtagtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcagATCATTAACGTATATAATCAGGAGTATGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTCCGTATCGTGATGGCACTGATTGTCTCACAGATAGTTT
upper sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G16230.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------------------------------gtaagtttcttcttcttt--ccttaatagggtcg-aatttgt---tttaaagcagtttcttaaacaaatttttgtttctg----tcagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC
|| || | | | || | ||| | || | ||| | | | | || || | | | |||||| ||||||||||||||||| ||||| || || ||||||| |||||| || ||||| || || ||| || || | ||| || | | |||||| | ||
gtacagagatgttaaatttatatatgcacgtttacgattctggtgccattaatcattcattaaaaaatgcacacaacacagttaacaccataatggcttatacattaatccctattatacattagcaccgtagtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcagATCATTAACGTATATAATCAGGAGTATGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTCCGTATCGTGATGGCACTGATTGTCTCACAGATAGTTT
upper sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------gtaagtttcttcttctttccttaatagggtcgaatttgttttaaagcagtttcttaaacaaatttttgtttctgtcagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC
||| | | | || | | | | | | | || | || | ||| | | |||||| | || ||||||||||| || ||||||||||| || ||||||| |||||| || ||||| || |||||||| || | || | ||| | | || |||||| ||||||
atcagaaaacccccataatcagattaattatttgctgttatgcctttttattttcagttgtctagtaaattttaccttgaggtattttttgataatg-cagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagggtcgaatttgttttaaagcagtttcttaaacaaatttttgtttctgtcagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC
ccttaat putative branch site (score: 4)
tttttgtttctgtc putative PPT
tttcttaaacaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcttcttctttccttaatagggtcgaatttgttttaaagcagtttcttaaacaaatttttgtttctgtcagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA