Sequence
atgc intronic sequence ATGC exonic sequencegtatatttcactttctctgtgaatatgtatctattcttttgtgattagtatggctttcatttgtcacagcaaaatttgaaataactactttatattttgattctttatatgattattctttgcatttctgcatgtatgtccactctcaagTGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAGTGTTTTTATGGCTTATGGCTGTTGGTACCATTCTCTGTGCTTCTTACTG
Basic information
species | Glycine max |
transcript | GLYMA09G39500.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 4
--gtatatttcactttctctgtgaatatgtatctattcttttgtgattagtatggctttcatttgtcacagcaaaatttgaaataactactttatattttgattctttatatgattattctttgcat-ttctgcatgtatgtccactctca-agTGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAGTGTTTTTATGGCTTATGGCTGTTGGTACCATTCTCTGTGCTTCTTACTG
|| || | || | |||| | ||| | ||| | ||| ||||| || || |||| | || | ||| || || | ||| || | | || | | | || | || ||| ||||||||| | || |||||| ||||| |||||||| |||||| |||||||| |||||||||||||||||||||||||| ||||| || |||||
gtaaatcttcaaagccttccaccacctgaaatcttgtgccatgtcctatgtaggttttttttttgtttca---aattttgtt----ttgtcttggaagttgttttttggccatagtatctaacatatgtatcgaatttgttttcaatttctcagTTTCGGTGCAGCTATACTCTCCAGACCGTCCTCTGGTTGATACTGCAGAGGTGTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTG
upper sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 4
gtatat--ttcactttctctgtgaatatgtatctattcttttgtgattagtatg-gctttcatttgtcacagc---aaaatttgaaataactactttatattttgattctttatatgattattctttgcatttctgcatgtatgtccactctcaagTGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAGTGTTTTTATGGCTTATGGCTGTTGGTACCATTCTCTGTGCTTCTTACTG
||| || || ||| | | | | | | ||| | || | | || | ||||| | | |||| ||||| ||| || ||| || | | || | | | | ||| | ||| || |||| |||||| ||||| |||||||| |||||| |||||| | ||||||||||| |||||||||||||| ||||| || |||||
gtaaattgtttgtcttcagttccatgctttgtgtcatctctgtgaatacatgggtgcctatgtttgtttaacttttcatatttttggtaacttgagtattggaaacttattttagtgcaaggtagctaacaggctaagttttcctttttttgtcagTCTTAGTGGAGCTGTACTCTCCAGATCGTCCTCTGGTTGATACTGCAGAGGTGTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTG
upper sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 3
-----gtat-atttcactttctctgtgaatatgtatctattcttttgtgat-tagtatggctttcatttgtcacagcaaaatttgaaataactactttatattttgattctttatatgattattctttgcatttctgcatgtatgtccactctcaagTGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAGTGTTTTTATGGCTTATGGCTGTTGGTACCATTCTCTGTGCTTCTTACTG
| | | | || | | || | | | | |||| | || | | || || | | | || |||| ||| | | | | | | | || | | || |||| || ||| || |||||| | || |||||| || || | ||||| |||||| |||||| ||||||||||||||||||| || | || ||||||| |||||
gtaaaatgttaacttaccgttgtcaccagcattttaatttccatttgaaacataaaggtgttaacacttaactgacccttcacctttatgtggacttgtcctttgttctatctgaaatagcttaccatgtactgacttatccttgtctcttccttagTTTCTGTGCAGCTTTACTCTCCAGATCGACCTGTAGTTGACACTGCAGAGGTGTTTCTATGGCTTATGGCTGTTGGCACAGTACTTGGTGCTTCCTACTG
upper sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatatttcactttctctgtgaatatgtatctattcttttgtgattagtatggctttcatttgtcacagcaaaatttgaaataactactttatattttgattctttatatgattattctttgcatttctgcatg-tatgtccactctcaagTGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAGTGTTTTTATGGCTTATGGCTGTTGGTACCATTCTCTGTGCTTCTTACTG
|||| || | || | || | ||| | ||| || ||| | | | |||| | || ||| | | || | | || | | | | ||||||| || || ||| | || ||| | ||||| | || || || |||||| |||||||| || || || ||| | |||||||||||||| ||||||||| | ||||||||||| ||
--------gtaattcttcgtataaatcaaactgtacttccgca--tagattgctcttcttgtattttagcatatcttatcatagtt---tggcatctctgtgctctctct---ttttctttgagttggtgttgactatatttgttc---agTTACTCTGCAGCTCTACTCGCCGAAACGTCCAGCAGTTGATGTGGCTGAGGTCTTTCTTTGGCTTATGGCTGTCGGTACCATTTTATGTGCTTCTTATTGMapped 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|193541082|gb|FK497826.1|FK497826EST: ACAAGATGCTGGTGAAAACTTGAAAAATCACATACTAAACAATTCAGTAG TGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAG
genomic: ACAAGATGCTGGTGAAAACTTGAAAAATCACATACTAAACAATTCAGTAGgtatatttca ... cactctcaagTGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgattctttatatgattattctttgcatttctgcatgtatgtccactctcaagTGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAGTGTTTTTATGGCTTATGGCTGTTGGTACCATTCTCTGTGCTTCTTACTG
ttttgat putative branch site (score: 4)
tccactctc putative PPT
ttctttatatgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatttcactttctctgtgaatatgtatctattcttttgtgattagtatggctttcatttgtcacagcaaaatttgaaataactactttatattttgattctttatatgattattctttgcatttctgcatgtatgtccactctcaagTGTCGGTGCAGTTGTATTCTCCATTGCGTCCATTGGTTGATGTTGCAGAAGTGTTTTTATGGCTTATGGCTGTTGGTACCATTCTCTGTGCTTCTTACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT