Sequence
atgc intronic sequence ATGC exonic sequencegtaaattcataataacattttgatgttacgaatctgatttaggtggttgttctatgaaatcttatctaatgatgatgttcatttgcagGTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTGAGGTCACCACTAAATGCTGAACAAAAAATGAGTACTCTTGAATCCTTGT
Basic information
species | Glycine max |
transcript | GLYMA08G19820.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G19820.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g28120.1 (Oryza sativa), 3'ss of exon 3
gtaaattcataataacattttgatgttacgaatctgatttaggtggttgttctatgaaatcttatctaatga-tgatgttcatt---------tgcagGTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTGAGGTCACCACTAAATGCTGAACAAAAAATGAGTACTCTTGAATC-CTTGT
|| | | | | ||| | | ||| | ||||||| | | | | || ||| | || || | ||||| | ||| | | || | || || || ||||| |||||| ||||||||||| | ||||||||||||||||| || || ||| || || || || ||||
gtgagtgtttggtttggctttcgcggcatagcattgaacttta-ggttgttatgtaaggtattgatagatggctaatatttgtgaattgtgaatgcagTTAGATGCAAGGTTCTGCATCCCTTGCTTGGAAGAGGTTTTGATCACAGTGCGCTCACCACTAAATGCTGAGCAGAAGCTGAACACCCTCGAGTCGCTTG-
upper sequence: GLYMA08G19820.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G10780.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaattcataataacattttgatgttacgaatctgatttaggtggttgttctatgaaatcttatctaatgatg--atgttcatt-----tgcagGTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTGAGGTCACCACTAAATGCTGAACAAAAAATGAGTACTCTTGAATCCTTGT
||||| ||||| | | || || | || || ||| || | | |||||| ||| ||| | | |||| ||||| | || | |||||| ||| || ||||||||||||||||| ||||||||||| || ||||| || || ||||| || |||| || |||||||| |
gtaaaa--ataatctcttcttcat--cagaaaccttccttaccgatgaagtcaaagcctacttatc-aataatgtaacctccattctctttgcagCTTGAGACCGGATTTACAATACCGTGTTTGGAGGAGGTTGTTATCACAGTGAGATCTCCACTGAACGCAGAACAGAAGATGAACACGCTTGAATCACTAG
upper sequence: GLYMA08G19820.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0034g01430.t01 (Vitis vinifera), 3'ss of exon 2
gtaaattcataataacattttgatgttacgaatc-tgatttaggtggttgttcta----tgaaatcttatctaa---tgatgatgttcatt--tgcagGTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTGAGGTCACCACTAAATGCTGAACAAAAAATGAGTACTCTTGAATCCTTGT
||||||| || | | ||| ||| || | ||||| | || || || | | || ||| | || || | | |||||| ||||||||||| | | ||| | ||||||||| | |||||||| || |||||||||| |||||| ||||||||||||| |||||||| ||||| ||||| |
gtaaattgatgagatcataacaatgctattccccctgattcaaaaggatgctcaaaatttagcattttaacaaagattggtctttttcattcttgcagGTGGATTCAAGTTTTGTGATTCCATGTCTAGAGGAGGTGCTGGTCACAGTGAGATCACCATTAAATGCTGAACAGAAAATGAGCACTCTAGAATCACTACMapped 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|58021949|gb|CX708690.1|CX708690EST: TCCATGGAGCCATGTTTGCAGCACTTTGCCAGAGGAACAGCCTGAAACAT GTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTG
genomic: TCCATGGAGCCATGTTTGCAGCACTTTGCCAGAGGAACAGCCTGAAACATgtaaattcat ... tcatttgcagGTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTG
EST:
gi|20814326|gb|BQ298804.1|BQ298804EST: TCCATGGAGCCATGTTTGCAGCACTTTGCCAGAGGAACAGCCTGAAACAT GTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTG
genomic: TCCATGGAGCCATGTTTGCAGCACTTTGCCAGAGGAACAGCCTGAAACATgtaaattcat ... tcatttgcagGTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgatttaggtggttgttctatgaaatcttatctaatgatgatgttcatttgcagGTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTGAGGTCACCACTAAATGCTGAACAAAAAATGAGTACTCTTGAATCCTTGT
atctaat putative branch site (score: 3)
ttcattt putative PPT
aaatcttatctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattcataataacattttgatgttacgaatctgatttaggtggttgttctatgaaatcttatctaatgatgatgttcatttgcagGTGGATCCGGGATTTTTAATTCCATGTTTGGAGGAGGTTGTGATCACAGTGAGGTCACCACTAAATGCTGAACAAAAAATGAGTACTCTTGAATCCTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG