Sequence
atgc intronic sequence ATGC exonic sequence...ataacaactcaagttgtgtgccttttcagagtgtgttgacctctgtcctgtcttttcttttttccttttctaacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
Basic information
species | Glycine max |
transcript | GLYMA01G01990.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G01990.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G115456_T01 (Zea mays), 3'ss of exon 1
----ataacaactcaagttgtgtgccttttcagagtgtgttgacctct-gtcctgtcttttcttttttccttttctaacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
||| | || | | || | || || || | ||| | ||| | || | | | |||||| | | || | | ||||| || || |||||||||||||| | |||||||||||||||||||||||| ||| || || ||||| |||| | || ||| | || | |||||
tcacatatgatctgcactctactggcaattggaag-atgctattttctcagcaaacaatttatattgcaccctaacgatgtcatctgtgcctttttac----cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: GLYMA01G01990.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
ataacaactcaagttgtgtgccttt-----tcagagtgtgttgacctctgtcctgtcttttcttttttccttttctaacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
|| | | ||| | | || | || ||| || | || | || | | | ||||| | | || | | ||||| || || |||||||||||||| | |||||||||||||||||||||||| ||| || ||||| || |||| | || ||| | || | |||||
-ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttcttac----cagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: GLYMA01G01990.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G17750.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------ataacaactcaagttgtgtgccttttcagagtgtgttga----cctctgtcctgtcttttcttttttccttttctaacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
| | | | ||||| || || | ||||| || || || | | || | ||| || | || | | | ||||||||| ||||| || ||||||||||| ||||||||||| ||||| ||||| || | |||||||| || | | | || || | || ||||| |||
gtaagtataaattctctcgcgccctaatttctccaccattgatttctctaattgtactgtgtatagattatgatttcgttgaataatcttagtgcttgatgtgtttgataagatttatatgattcatgtgccaattttgatgaacagGGTTTTAGGAAAGTGGATCCAGATCGATGGGAATTTGCTAATGAAGGTTTCTTAAGAGGTCAAAAACATCTATTGAAGAAGATAAGCCGGAGAAAATCTG
upper sequence: GLYMA01G01990.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G32330.1 (Arabidopsis thaliana), 3'ss of exon 1
ataacaactcaagttgtgtgccttttcaga-gtgtgttgacctctgtcctgtcttttctttt----ttccttttc-taacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
| || | || | | | || || | ||| ||| || | | | | | | ||||| | | | | | || || | ||||||||||||||||||||||| |||||| | ||||||||||| ||||| |||||||| | ||||| ||||||||||| || || | ||||||||||
------gttttagatttgcacttctaaagctgtcggatgaattctttctcattggtcttggtggaatccattttcattccattttgcgtgtcttttcttgatacagGGTTTCAGGAAGGTTGACCCAGATAGATGGGAATTTGCGAATGAAGGTTTTTTAAGAGGTCAGAAGCACTTGCTACAATCAATAACTAGGCGAAAACCTG
upper sequence: GLYMA01G01990.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0012g01810.t01 (Vitis vinifera), 3'ss of exon 1
-ataacaactcaagttgt--gtgccttttcagagtgtgttgacctctgtcctgtcttttcttttttccttttctaacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
| | | || | | || || | | || ||| || || | |||| || | ||| ||| | || | |||||| |||||||||||||||||||| || |||||||||||||||||||| ||||||| ||||||||| ||| | | |||||||| | || ||||||||||
ttttattttgtatgtaatcaaagtctctttgtattctgctgattatagtttccctttcttccccatcctattttc---ctatcttgtcactgtctgcaaacagGGATTCAGGAAGGTTGATCCAGACCGTTGGGAATTTGCAAATGAGGGATTTTTGAGGGGTCAAAAACACCTATTGAGGAGTATAAATCGGCGAAAACCTGMapped 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|298179085|gb|HO027556.1|HO027556EST: ACTTTAAACACAACAACTTCTCCAGCTTCGTTAGACAGTTAAACACTTAC GGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTT
genomic: ACTTCAAACACAACAACTTCTCCAGCTTCGTTAGACAGTTAAACACTTACgtatgtttcc ... cattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTT
EST:
gi|193329021|gb|FK293025.1|FK293025EST: ACTTCAAACACAACAACTTCTCCAGCTTCGTTAGACAGTTAAACACTTAC GGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGG
genomic: ACTTCAAACACAACAACTTCTCCAGCTTCGTTAGACAGTTAAACACTTACgtatgtttcc ... cattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgtcttttcttttttccttttctaacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
ttctaac putative branch site (score: 1)
aattcattatcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataacaactcaagttgtgtgccttttcagagtgtgttgacctctgtcctgtcttttcttttttccttttctaacgtcatcaattcattatcattatacagGGTTTCAGGAAGGTTGATCCAGATCGCTGGGAATTTGCAAATGAGGGTTTTTTGAAGGGTCAAAAGCACTTGCTTAGGAGTATTACACGACGAAAACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - caactca
- - - - - - - tgtgtgc
- - - - - - - - - - - - - - gagtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caattca