Sequence
atgc intronic sequence ATGC exonic sequence...ataatgcatttgttctttctgcttggcactatgctactaataaaaaatcatggtcatgattaattctttttctggtaacaacaatttttttatgttgaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA
Basic information
species | Glycine max |
transcript | GLYMA19G02360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------------------------------------------ataatgcatttgttctttctgct--tggcactatgctactaataaaaa-atc--atggtcatgattaattctttttctggtaacaacaatttttttatgttgaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA
|| | | || | | || | | ||| |||| || ||||| || || | | | || | | || | | | ||| ||| |||| | || ||||| |||||||| ||||||||||| |||| ||||| ||||| || ||||||||||| || |||||||| || | || || | || ||
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctat-----agGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
---ataatgcatttgttctttctgcttgg---cactatgctactaataaaaaatcatggtcatg-attaattctttttctggtaacaacaatttttttatgttgaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA
| ||||| | ||| || || ||| ||| | || | ||| || ||| || | | || | |||| | ||| |||| | | ||||| || ||| | |||||||||| ||| ||||||||||| || || || ||||||||||| |||||||| ||| | ||||| | || ||
gttgcgttaaatttggcccaactgtttcatttcagtataactctattctgaagt----gtcttgtatttatctgatatttgtcttggataattgtattaaac---agGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA
upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
-ataatgcatttgttctttctgcttggcactatgctac--taataaaaaatcatggtcatgattaattctttttctggtaacaacaatttttttatgttga--agGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA
| | || || | | || | | | | | | || ||| || | | | | | ||| || |||| ||||||| | | | || | | ||||||| || ||| | || |||||||||||||| |||||||| || ||||| || |||||||| |||||||| ||| | || || |||| ||
aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaacct--tcacatacccatct---aataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
ataatgcatttgttctttctgcttggcactatgctactaataaaaaatcatggtcatgattaattctttttctggtaacaacaatttttttatgtt-gaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA
| || || || | | ||| | | |||| ||||| ||||||| | | | | ||| ||||| ||||| || |||||||||||||||||||| | ||||| |||||| | ||||| || |||||||| ||| ||||||||||| ||| || ||| | |||||
--------------------gtatgtataaatcaaaccattttaaagttgtttccatgtttaatcgtttttcttatgatactggtgctttcatgtttaaagGGTCCTTGCCTCTTCCTTGGTCTATCCGGATGAAGATTGCATTAGGTGCTGCAAAAGGTCTCAGTTTCCTCCATGAAGAAGCTTTGAAGCCTGTTATATA
upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 2
ataatgcatttgtt-ctttctgcttggcactatgctactaataaaaaatcatggtcatgattaattctttttctggtaacaacaatttttttatgttgaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA
| | | | | | || || | | | | | | | | | | || | || ||| || | | |||| || | ||||| ||||||||| | ||||||||||||||||||||||||| |||||||| || ||||| || ||||| ||| ||| ||| | |||||
---gtatgtctatcgcaaacctctgcacatcttcttctttctgagggctttgaggtgtc-tcgtctaattaccatgtttttcttttttcatttgggttcagGGACCTTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATAMapped 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|23733669|gb|BU765039.1|BU765039EST: GGTTTATGAGTTTATGCCCCGAGGCAGTTTGGAGAACCACCTCTTTAGAA GGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAG
genomic: GGTTTATGAGTTTATGCCCCGAGGCAGTTTGGAGAACCACCTCTTTAGAAgtactctact ... tatgttgaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcatggtcatgattaattctttttctggtaacaacaatttttttatgttgaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA
tggtaac putative branch site (score: 2)
tttttttat putative PPT
taacaacaattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataatgcatttgttctttctgcttggcactatgctactaataaaaaatcatggtcatgattaattctttttctggtaacaacaatttttttatgttgaagGGCCCCTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - tgcattt
- - - - - - - - ttctgct
- - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - catggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaca