Sequence
atgc intronic sequence ATGC exonic sequencegtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11130.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
-----------------------gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaac-ggta---atattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
|| | | || | ||||| | | ||||| | || ||| | | | | ||| | || | | | || | |||||||||| ||||| |||||||| ||||||||||| || ||||| || || || ||||| ||||| |||||||| || ||||||| |||||||| ||
gtaaaatgggtgttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
-----------------------gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaac-ggta---atattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
|| | | || | ||||| | | ||||| | || ||| | | | | ||| | || | | | || | |||||||||| ||||| |||||||| ||||||||||| || ||||| || || || ||||| ||||| |||||||| || ||||||| |||||||| ||
gtaaaatgggtcttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
--------------------gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattca--gACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
| | || | | || | || ||||| | | | | ||| ||| | | || | |||| | ||||||||| ||||| ||||| || |||||||||||||| || || || || || ||||| ||||| |||||||| || | ||||||||||||||||||
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
---------gtaatc-ttaaaatgaccattttcatttaaagtgtc---tcctatgggcttct---ttagtatgctgtaacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
|| | || | || || | || || | | || ||| | || || || | | | | | || |||||||||| ||||| ||||| || ||||||||||| || ||||| || || || ||||| ||||| |||||||| || | |||||||||||||| | |
tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT-----------------
|| || | | || | |||| | || || |||| | | | ||| || |||||||||| ||||| ||||| || ||||||||||| || ||||| || || || ||||| ||||| || ||||| || | |||||||||||||| |||
----------------------caatttacat-tcacttatgtattgatt--gtttgcta-agtgtgtgcactttt--atgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
-----------------------------gtaatcttaaaatg-accatt-ttcatttaaagtgtctcctatgggcttctttagt-atgctg--taacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
| | || | | | || | | | || || || | |||| | | || | || | | |||||| ||| | |||||||||||||||| ||||| ||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||| |||||||||||||||| ||
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
--------------------------------------------------------------------------gtaatct--taaaatgaccattttcatttaaagtgtctcctatgggcttctttagt-atgctg--taacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
| | || || || | | | || || || | |||| | | || | || | | |||||| ||| | |||||||||| ||||| |||||| ||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||| |||||||||||||||| ||
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 12
---------------------------------------------------------------------------------------gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctg--taacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
||| | | ||| |||| || ||| | | || | | || | | | | | || || | |||||||||| ||||| |||||| |||||||||| |||||||| ||||||||||||||||| ||||| || ||||| ||| | |||||||||||||||||
gttgggttgcattaaaattttgaaaaattcaatattattttgttatttataactttgcttgtactctatctttctaattgtctcccaaaaatataggggtactgattctcatctagcctgtttattgtgaaatgttgtattctattaatttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCATTTGCTGAGAGGAGGGAGTTTGACAAAATTC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
-------------------------------------------------------------------------------gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
|| || | ||| |||| ||| ||| | | || | | || || || | || || | || | |||||||||| ||||| |||||| |||||||||| |||||||| ||||||||||||||||| ||||| || ||||| ||| | |||||||||||||||||
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaaatagggtactgattctcatctaacctgtttattgtgaaatgttgtatta-acttttacaagcatgctcccttgt--agACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 12
--------------------------------------------------------------------------gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgt-aacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
| | ||| | | | | | ||||||| | | | | | | | || | | || |||| | | |||||||||||| ||||||||| || |||||||| || ||||| ||||| ||||| ||||| |||||||| ||||| ||||| ||||||||||||||||
gtttgaaatgcaattggagatgattattttttgtccacttaagacaattcttgttgggatgctaatttgagtttattttattatttttatcctgctaatttaaatgatttttttttttaaatataattttgacattgaaaaccatgttttttt-tgtagACTGTGGATACTGACCTTGCACTCAAAATATATATTAAAGCGAGAGCAACTCCGAAAGTTGTTGCAGCCTTTGCTGAGCGTCGGGAGTTTGACAAAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
ttctgat putative branch site (score: 3)
tattttct CT-rich tract
taatattttctgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcttaaaatgaccattttcatttaaagtgtctcctatgggcttctttagtatgctgtaacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT