Sequence
atgc intronic sequence ATGC exonic sequence...ttatgcaccaaaacatgaacaaaacgatactgttatgttcaattgatataatcatcatattactttctattattttgacacatttgtttaacttatgcagATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGGTGGTCTCTTGCAGATTCAAAGTATGCAGGGACAGCACTACTGGTGAAAA
Basic information
species | Glycine max |
transcript | GLYMA04G36610.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G36610.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G170291_T01 (Zea mays), 3'ss of exon 2
ttatgcaccaaaacatgaacaaaacgatactgttatgttcaattgatataatcatcatattactttctattATTTTGACACATTTGTTTAACTTATGCAGATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGGTGGTCTCTTGCAGATTCAAAGTATGCAGGGACAGCACTACTGGTGAAAA
| | | | | | | || || || ||| | | || | || || | || || | || || | | | |||| | | |||||| | || ||| ||||||| |||| | || |||||||||||| |||||||||| ||||| |||||||| | | | || |
tcctagattatgatttctatctgtgtcgtttgctacattggattcagtggcttgacaacaaaattgttacattactgtcatacttcttgatgtcaagcagGTAGTTCTACGTGCTTTGTCAGCTTCACCTTTCAAAGACTACCGTGTCTGGTGGTCTCTTTCAGATTCAAAATATGCTGGGACAGCTATGTTTATAAAGA
upper sequence: GLYMA04G36610.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G48425.1 (Arabidopsis thaliana), 3'ss of exon 2
ttatgcaccaaaacatgaacaaaacgatactgttatgttcaattgatataatcatcatattactttctattATTTTGACACATTTGTTTAACTTA---TGCAGATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGGTGGTCTCTTGCAGATTCAAAGTATGCAGGGACAGCACTACTGGTGAAAA
|| ||| ||| | | | || | || | | | | || || ||| | | | | | || |||||| |||||||||||||||| || || || |||||| ||||| || ||| |||||||||||||| || || || ||||||||||||||||| | | |||||||
--attt-taaaagaatgcgggagccacttatggagtaacaaactctcttgttgtttggataacattcaagcttgatattagttctgggaaacttaacttgcagATTTTGACACGGGCTCTCTCAAGTCCACCATTTGGAAATTATGGGGTTTGGTGGTCTCTCGCGGACTCGAAGTATGCAGGGACAGCTTTGTTAGTGAAAA
upper sequence: GLYMA04G36610.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g09970.t01 (Vitis vinifera), 3'ss of exon 2
-ttatgcaccaaaacatgaacaaaacgatactgttatgttcaattgatataatcatcatattactttctattATTTTGACACATTTGTTT-AACTTATGCAGATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGGTGGTCTCTTGCAGATTCAAAGTATGCAGGGACAGCACTACTGGTGAAAA
|| || | | ||| | || ||| ||||| | || | ||| || || | | | | |||| ||| | |||||||| || | | ||| ||||| || || ||||| || |||| ||||||||||||||||||||||| || ||||||||||| ||| | | || || |
tttgggctctgtgagttgagttgtggaaatttggtat-ttcaac-gctaagaaaatcggatatctactaacagcaattatatatttcttttgaaccatgcagATATTAATGCATGCCCTTTCCAGACCTCCATTTGGAAATTATCGTGTTTGGTGGTCTCTTGCAGATTCCAAATATGCAGGGACTGCATTGTTTGTTAAGAMapped 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|207765988|gb|GD735517.1|GD735517EST: CGGCCGGGGAAGAAAAGAAG ATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGG
genomic: CGGCCAGGGAAGAAAAGAAGgtacctttat ... acttatgcagATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGG
EST:
gi|207710620|gb|GD691304.1|GD691304EST: CGGCCGGGGAAGAAAAGAAG ATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGG
genomic: CGGCCAGGGAAGAAAAGAAGgtacctttat ... acttatgcagATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGG
EST:
gi|193490821|gb|FK455946.1|FK455946EST: GAAGAAAAGAAG ATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGG
genomic: GAAGAAAAGAAGgtacctttat ... acttatgcagATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atataatcatcatattactttctattattttgacacatttgtttaacttatgcagATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGGTGGTCTCTTGCAGATTCAAAGTATGCAGGGACAGCACTACTGGTGAAAA
gtttaac putative branch site (score: 3)
atcatattactttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgcaccaaaacatgaacaaaacgatactgttatgttcaattgatataatcatcatattactttctattattttgacacatttgtttaacttatgcagATTTTGACACGTGCACTTTCTGCTCCACCTTTTGGGAACTATCACGTTTGGTGGTCTCTTGCAGATTCAAAGTATGCAGGGACAGCACTACTGGTGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT