Sequence
atgc intronic sequence ATGC exonic sequence...ccatacaatctatcttttcgttttgcctttcattgtctctgtagtttatctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12100.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g58580.1 (Oryza sativa), 3'ss of exon 2
-----ccatacaatct-atcttttcgttttgcctttcattgtctctgtagtttatctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
|| || || | | | || || | |||| || | | | | | || | || | | | || | | | ||||||||| ||||| | ||| |||| |||||||| ||||| ||||| || ||||||||||| |||||||| || ||||||||
tgtgatttcaccataggattgctaggcaaaactcctcctttttatattagtatagatatattttgaccacctccatccatatgcttctt--ctttgttctagACAGCTCTTCCTGCTCTTCCTGTCTTTCTCCTTGGCTGTTGAAGCACTACATGCATTTATGCAAGATGAGTCTGAGCATAA
upper sequence: AT3G12100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G017365_T09 (Zea mays), 3'ss of exon 2
------ccatacaatctatcttttcgttttgcctttcattgtctctgtagtttatctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
| | | | | ||| || | ||| | | ||||| ||| |||| || ||| | ||||| ||| | | | |||||||||||||| || ||||| |||| |||||||| ||||| ||||| | ||||||||||| ||||||||||| ||||| ||
tgccggaaaaaaacaccctgtttgtattacacttttaaccctttctgtccttttgctttgtg-ctaacattttgaccaccaccctatg-gttctttatgtagACAGCTGTTTCTATTGTTCCTGTCTTTCTCCTTGGCTGTTGAAGCATTACATGCATTTATGCAAGATGAATCGGAGCACAA
upper sequence: AT3G12100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G017365_T08 (Zea mays), 3'ss of exon 3
--ccatacaatctatcttttcgttttgcctttcattgtctctgtagtttatctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
| | | | | ||| || | ||| | | ||||| ||| |||| || ||| | ||||| ||| | | | |||||||||||||| || ||||| |||| |||||||| ||||| ||||| | ||||||||||| ||||||||||| ||||| ||
ggaaaaaaacaccctgtttgtattacacttttaaccctttctgtccttttgctttgtg-ctaacattttgaccaccaccctatg-gttctttatgtagacagCTGTTTCTATTGTTCCTGTCTTTCTCCTTGGCTGTTGAAGCATTACATGCATTTATGCAAGATGAATCGGAGCACAA
upper sequence: AT3G12100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G30140.1 (Glycine max), 3'ss of exon 3
-ccatacaatctatcttttcgttttgcctttcattgtctctgtagtttatctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
|| | | || || | || | || | | | ||| | | | ||| | |||| || | | | | || |||||||||||||||| ||| |||| |||||||||||| |||| || || || ||||||||||| |||||||||||||||||||| ||
taactatggcaaacttatttcattcttttctcttgttcggtacattacatcatgtgcgctaacatcttgaattttcttgt-tctgctgcctgtgtagacagCTGTTTCTTTTGTTTATGTCATTCTCCCTAGCAGTTGAGGCACTTCATGCATTCATACAAGATGAATCAGAGCACAA
upper sequence: AT3G12100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G33030.1 (Glycine max), 3'ss of exon 3
ccatacaatctatcttttcgttttgcctttcattgtctc-tgtagtttatctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
| | | ||| || || ||| | | | | ||| | | | ||| | |||| || | | | | || ||||||||||||| || ||| |||| |||||||||||| |||| || || || ||||||||||| |||||||||||||||||||| ||
taactatggcaaacttaattcattattttctcctgtttggtacattacatcatatgcgctaacatcttgaattttcttgt-tctgctgcttgtgtagacagCTATTTCTTTTGTTTATGTCATTCTCCCTAGCAGTTGAGGCACTTCATGCATTCATACAAGATGAATCAGAGCACAA
upper sequence: AT3G12100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g06550.t01 (Vitis vinifera), 3'ss of exon 3
-ccatacaatctatcttttcgttttgcctttcattgtctctgtagtttat--ctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
| || ||| | | || | ||||| | ||| | || | | | | ||| | | || | ||| || | || |||| |||||||||||| || |||| |||||||||||||| ||||||||||| ||||||||||| |||||||||||||| ||||| ||
ttttcatcat-tatgtgattattgttgtcatcatttttcttgttggttgctgcctctagactaacatgtaaatat-tttgat-tctgctgcatgtttagacagCTGTTTCTGTTGTTTATGTCATTCTCCTTGGCTGTGGAAGCACTTCATGCATTCATACAAGATGAATCTGAGCACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
atttgac putative branch site (score: 4)
ttaatactttgatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatacaatctatcttttcgttttgcctttcattgtctctgtagtttatctttttggttaatactttgatttgtttaatatttgacatatgtgtagacagCTGTTCCTTATGTTCATGTCATTCTCCTTAGCTGTGGAAGCTCTTCATGCATTTATACAAGATGAATCAGAGCATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
-catacaa
- - - - - - - - - - - - - - - - - gtctctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatttgt