Sequence
atgc intronic sequence ATGC exonic sequencegtgtgatctcctttctatgtgtttaaaatctttttgtctgtttgcttatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G56110.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
----gtgtgatctcctttctatgtgtttaaaatctttttgtctg--tttgcttatctcatatggtt-tgtgttctcataaaaaatttctgtttat-gtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
| || ||| || | | | ||| | | | || | || | | || | |||| | | || | | || | |||| ||| | ||||| ||||||| || | | || ||||| ||||| || ||||| ||||||||||| ||||| |||||||||||||| |||||||
tgttggactgcaatgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgttttcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 2
--gtgtgatctcctttctatgtgtttaaaatctttttgtc-tgtttgcttatctcatatg-gtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATC-----TTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
| | || | | | |||| |||| || | || | | || | || | || || ||| ||| || || | | ||| | || || | |||||||| | | ||| ||||||||||| || ||||||||||||||||| ||||| || || |||||||| ||||| |
caaagaaaaatcttgtatgtgtgcttaagttcaaaatctcgtaaagaaaaaatgtatgtacacccgtttgcttattctggttttgtgtg-atttactttagAAATCGGACTTGGAGAAGGCGCAGCTTGGCCTGGGTCATAGCTACAGCAGGGCGAAGGTGAAGTTCAATGTGAACCGCGTTGACAACATGGTGATTCAGG
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 2
--------gtgtgatctcctttctatgtgtttaaaatctttttgt-ctgtttgcttatctcatatggtttgtgttctcataaaaaatttctgtttat-gtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
| | | |||| ||| || |||| | || | || || | | |||| || | | | |||| || |||| | ||| | || || | || ||||| | | || ||||||||||| || ||||||||||||||||| || || || ||||||||||| || ||||
tgatgagcttacgcattgctttttatatgcctaaattgttgtaaagctaaacgcctgctgtgcttaatttggcttt--accatgtgtccatgttgattgtagGATTCTGACTTGGAGAAGGCCCAACTTGGCCTGGGGCATAGCTACAGCAGGGCTAAGGTGAAGTTCAATGTGAATCGTGTTGATAACATGGTGATCCAAG
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 2
-------------gtg-tgatctcctttctatgtgtttaaaatctttttgtctgtttgcttatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
|| || || | || |||| | |||| || |||| ||| | | || || || | | | | | | | ||||| | ||| | || || | |||||||| | | || ||||||||||| |||||||||||||||||||| || || || || |||||||| || || |
tgcaaaattttggctgctgggcttatgcata-gtgtatcaaattttgttgtgaagttggatgcttgatgtgcttaatttgtttttccgatggtgat-----tgtagGATTCTGACTTGGAGAAGGCCCAGCTTGGCCTGGGGCATAGCTACAGCAGGGCCAAGGTGAAGTTCAATGTGAATCGTGTTGACAACATGGTGATCCAGG
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 2
----------------gtgtgatctcctttctatgtgtttaaaatctttttgtctgtttgcttatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
| | | | | | | ||||| | || | |||| || | | | | | | | | | | | ||| || |||| ||| | ||||| | || ||||| | | || || ||||||||||| ||||||||||| ||||||||||| || || ||||||||||||||||
gttagtgtttcctcatgcctctttttgtgtttctgtgtgcaggataactgtgtcctatttttatcactaatttatatatatattttttatgctgcttgattttcacagTCTGGAGATTTAGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAGTTTAATGTTAACCGTGTTGACAACATGGTTATTCAAG
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
----gtgtgatctcctttct-atgtgttt----------aaaatctttttgtc-tgtttgcttatctcatatggtttgtgttctcataaaaaatttctgt-----------ttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
| | ||||| || ||||||| | |||| ||| | | | ||| | || | || | || | ||| | | || ||||| | || ||| | ||||| | || ||||| | | || || ||||||||||| |||||||| |||||||||||||| || || |||||||| |||||||
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttattttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
----------------gtgtgatctcctttctatgtgtttaaaatctttttgtct-gtttgcttatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
| | | | | | | ||| | | | | | ||| ||| | || || | | |||| | | || ||| || |||| ||| | ||||| | || ||||| | | || || |||||||| || ||||||||||| ||||||||||| || || ||||||||||||||||
gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctg--cttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------gtgtgatctcctttctatgtgtttaaaatctttttgtctgtttgct-tatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
| || | | | ||||| | | | | || || || ||| | | || | | ||| ||| | | | | | |||||||||| || || ||||| | || ||||| | | ||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| ||||| ||||| |
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaattt-ctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGG
upper sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S88_119V6.1 (Physcomitrella patens), 3'ss of exon 2
--gtgtgatctcctttc-tatgtgtttaaaatctttttgtctgtttgc------ttatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
| | | | |||| | | | || |||||||| |||| | || || | || || | | | | | | | || |||||||| || ||| |||| || | || || || | |||||||| ||||| | || || |||||||||||||||||||| ||||||||| | ||||||
ttgaattgccgcttttcacaaatatctacgtgctttttgtatgttggtgtgcaattgactttcacatttagtataccta-agatggtgtttggttatgtagGAGGGAGATATTGAGAAGGCGCAACTCGGTCTTGCTCACAGTTACAGTCGCAGTAAAGTTAAGTTCAATGTTAACCGAGTAGATAACATGATCATTCAAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|47829863|gb|CK119547.1|CK119547EST: TTCTCAGAGGTGTTCGCCAGCATTTTGATAGGTTTATCAAGGACTTAAAG CCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGA
genomic: TTCTCAGAGGTGTTCGCCAGCATTTTGATAGGTTTATCAAGGACTTAAAGgtgtgatctc ... gtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGA
EST:
gi|116482901|gb|EG525493.1|EG525493EST: TTCTCAGAGGTGTTCGCCAGCATTTTGATAGGTTTATCAAGGACTTAAAG CCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGA
genomic: TTCTCAGAGGTGTTCGCCAGCATTTTGATAGGTTTATCAAGGACTTAAAGgtgtgatctc ... gtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtttgcttatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
tttctgttt CT-rich tract
ataaaaaatttctgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgatctcctttctatgtgtttaaaatctttttgtctgtttgcttatctcatatggtttgtgttctcataaaaaatttctgtttatgtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA