Sequence
atgc intronic sequence ATGC exonic sequence...atgttcaactcaaagattcactgtgcacagtttctcaacaaagatttgatgttttttttttctttttctcttttatctcctataattcggattctctcagGCCTGGGGTTGGCAAAACTACTGTTATGCGAGAGATTGCTCGTGTACTGTCTGATGAGCTTCACAAAAGAGTG
Basic information
species | Glycine max |
transcript | GLYMA20G35550.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35550.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g10640.1 (Oryza sativa), 3'ss of exon 4
--------atgttcaactcaaagattcactgtgcacagtttctcaacaaagatttgatgttttttttttctttttctcttttatctcctataattcggattctctcagGCCTGGGGTTGGCAAAACTACTGTTATGCGAGAGATTGCTCGTGTACTGTCTGATGAGCTTCACAAAAGAGTG
|||| | ||| || ||| ||| || | || || || |||| | | ||| ||| | | | | ||| |||||||||||||||||| |||||||||||||| |||||||| ||||| || | ||||| |||| |||||||||
gtccactcatgtccc-ttcagggactcag---gcaaggtgt---ggtgtagtcatg-tgcattttaatgcaatttgaaatttcattgatttgtgttttatttggccagGCCTGGGGTTGGCAAGACTACTGTTATGCGTGAGATTGCACGTGTTCTAGCAGATGAATTTCAGAAAAGAGTG
upper sequence: GLYMA20G35550.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G162800_T03 (Zea mays), 3'ss of exon 4
------atgttcaactcaaagattcactgtgcaca--gtttctcaacaaagatttgatgttttttttttctttttctcttttatctcctataattcggattctctcagGCCTGGGGTTGGCAAAACTACTGTTATGCGAGAGATTGCTCGTGTACTGTCTGATGAGCTTCACAAAAGAGTG
| | | | |||| | | ||| |||| |||| || ||| | ||| | | | || ||| || | ||| ||||||||||||| ||||| |||||||||||||| |||||||| ||||| | | ||||| |||| |||||||||
atagggaaacaggagttgagcattccgtttccactttgtttttcaaataaattttcaaaagtttatctgttcttcaatatttttccttttc--------ttcaatcagGCCTGGGGTCGGCAAGACTACTGTTATGCGTGAGATTGCGCGTGTTTTAGCAGATGAATTTCAGAAAAGAGTG
upper sequence: GLYMA20G35550.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G162800_T02 (Zea mays), 3'ss of exon 5
----------------atgttcaactcaaagattcactgtgcaca--gtttctcaacaaagatttgatgttttttttttctttttctcttttatctcctataattcggattctctcagGCCTGGGGTTGGCAAAACTACTGTTATGCGAGAGATTGCTCGTGTACTGTCTGATGAGCTTCACAAAAGAGTG
| | | | |||| | | ||| |||| |||| || ||| | ||| | | | || ||| || | ||| ||||||||||||| ||||| |||||||||||||| |||||||| ||||| | | ||||| |||| |||||||||
gtatgtgataatagggaaacaggagttgagcattccgtttccactttgtttttcaaataaattttcaaaagtttatctgttcttcaatatttttccttttc--------ttcaatcagGCCTGGGGTCGGCAAGACTACTGTTATGCGTGAGATTGCGCGTGTTTTAGCAGATGAATTTCAGAAAAGAGTG
upper sequence: GLYMA20G35550.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G33290.2 (Arabidopsis thaliana), 3'ss of exon 4
atgttcaactcaaagattcactgtgcacagtttctcaacaaagatttgatgttttttttttctttttctcttttatct----cctataattcggattc-tctcagGCCTGGGGTTGGCAAAACTACTGTTATGCGAGAGATTGCTCGTGTACTGTCTGATGAGCTTCACAAAAGAGTG
||| | || | ||| | | ||| || ||| || | || | | | | | ||| | | ||| | |||||||| ||||| || || |||||| ||||||||||||||||||| |||||||||| | || |||||||||
-----------------gtacttgttgcttgttttacacactactctaatgcttcatttctcatctttgatgatgatttaaacttctaaatggaattgataatagGCCTGGTGTTGGTAAGACCACTGTTTTGCGAGAGATTGCTCGTGTCTTGTCTGATGAATTCCAGAAAAGAGTGMapped 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|51338386|gb|CO982252.1|CO982252EST: ATGGTTTATGATCTGCTTCAGTATGGGAAGAGCATTTTATTTGTTGGAAG GCCTGGGGTTGGCAAAACTACTGTTATGCGAGAGATTGCTCGTGTACTGTC
genomic: ATGGTTTATGATCTGCTTCAGTATGGGAAGAGCATTTTATTTGTTGGAAGgtatataaca ... attctctcagGCCTGGGGTTGGCAAAACTACTGTTATGCGAGAGATTGCTCGTGTACTGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatgttttttttttctttttctcttttatctcctataattcggattctctcagGCCTGGGGTTGGCAAAACTACTGTTATGCGAGAGATTGCTCGTGTACTGTCTGATGAGCTTCACAAAAGAGTG
atttgat putative branch site (score: 5)
ttctctc putative PPT
ttttttttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgttcaactcaaagattcactgtgcacagtttctcaacaaagatttgatgttttttttttctttttctcttttatctcctataattcggattctctcagGCCTGGGGTTGGCAAAACTACTGTTATGCGAGAGATTGCTCGTGTACTGTCTGATGAGCTTCACAAAAGAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - -caactca
- - - - - - - - - - - -tgcacag
- - - - - - - - - - - - - - - - -ctcaaca