Sequence
atgc intronic sequence ATGC exonic sequence...tttaagtttgcccaatggcatcgtgtagcccatgtagctgacttcacttgttgttagtatttgcctatttggaaattcattttcatgcttttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGACGATGACGATTACTTTGATG
Basic information
species | Glycine max |
transcript | GLYMA08G19780.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G19780.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g18630.1 (Oryza sativa), 3'ss of exon 1
tttaagtttgcccaatggcatcgtgtagcccatgtagctgacttcacttgttgttagtatt-tgcctatttggaa-attcattttcatgcttttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGACGATGACGATTACTTTGATG
|| | | || |||||| ||| || | | | ||| || | ||| |||| | || | | ||| | |||||||| | | || || || || || ||||| || || | || |||||||||||||||||| || ||||||||||| || ||||| |||||||||||||
-caaaatatctgttattccatcgtactgcc-atattaatttgtgagtttgatgactggattgcatatattcatcatatgcctcttcttttaaaatgttgcagCTGGCAACAGGTGGTGGCGGTGGTGATATTGGGAAAAGGATTGGTCATGGTGGTGGTGATGGTGGAGATGATGATGGCGATGATGATGATTACTTTGATG
upper sequence: GLYMA08G19780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G016457_T01 (Zea mays), 3'ss of exon 1
-tttaagtttgcccaatggcatcgtgtagcccatgtagctgacttcacttgttgttagtatttgcctatttggaaattcattttcatgcttttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGACGATGACGATTACTTTGATG
|| | | || | | | | | | || | || | | || ||| ||| || | || ||| || | || ||||| | | || || ||||| |||||||| ||||| | ||| ||||||||| |||||||| |||||||||||||| |||||||| || ||||||||||
cttcatggttaggacacagtaacaaattgtgatggtcatgtgcatcgttaagt-ttcctatctgcataatactaatcacatatttcctttcaaaattccagCTGGCGACAGGTGGTGGTGGTGGAGATATTGGAAAAAGGATCGGTCATGGTGGGGGTGATGGTGGTGATGATGATGGTGACGATGATGACTACTTTGATG
upper sequence: GLYMA08G19780.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G24690.1 (Arabidopsis thaliana), 3'ss of exon 1
---tttaagtttgcccaatggcatcgtgtagcccatgtagctgactt-cacttgttgttagtatttgcctatttggaaattcattttcatgcttttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGACGATGACGATTACTTTGATG
| | || | | | | || | || | || || ||| | | | || | || | || |||| |||| ||| || ||| | | | ||| ||||| || ||| | || ||||||| |||||| |||||||||| ||||||||||| ||| |||| || ||||| |||||||||||||
gaatgatatcttccttggagataaca-gtttgcagtgaatctattttgcaccgatcagaaaagagtagctttgtgaatttttattt-catg--tttcattacagATTGCAACTGGAGGAGGGGGTGGAAACATTGGAAAGAGTATCAATAATGGTGGTGGCGATGGAGGTGACGATAATGGTGATGATGATGATTACTTTGATG
upper sequence: GLYMA08G19780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S309_83V6.1 (Physcomitrella patens), 3'ss of exon 1
tttaagtttgcccaatggcatcgtgtagcccatgtagctgacttcacttgttgttagtatttgcctatttggaaattcattttcatgcttttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGACGATGACGATTACTTTGATG
||| || | | | | ||| || || || | | | ||| | | || | | || || ||||| | || |||| || ||||| |||| ||| ||||| || | | |||| ||||||||||||||||| |||||||| |||||||| || ||||| | ||
cttatcctttcgcttaaatgtgatctaggttctgcgtttggtaatttgcgtaggtctaagttggtcaaggtggttggaatggcaacgtttgggtgtgcagGTGGAACTTGGTGGTGGTGGTGGAGGTATTGGAAATAAGAATTTTAATGGGGGTGGTGATGGAGGTGACGATGATGGCGACGATGATGACTACTTCGGTG
upper sequence: GLYMA08G19780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S57_231V6.1 (Physcomitrella patens), 3'ss of exon 1
tttaagtttgcccaatg-gcatcgtgtagcccatgtagctgacttcacttgttgttagtatttgcctatttggaaattcattttcatg---cttttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGACGATGACGATTACTTTGATG
||||| ||| | | || || | | | | || | ||| | | || || ||| | || ||| ||| | |||||| | || |||| || ||||| || | ||| || || || | |||| ||||| |||||||||||||||||||| || |||||||| ||||||| ||
---aagttctccctttttggataaagttgtcttagggttttgttttaag-attgcttgatttggcagggcgtgaacgtggagttgatgagacttgtaattgcagGTGGAACTTGGAGGCGGTGGTGGCGGTATTGGGAATAAGAATTTCAATGGAGGTGGAGATGGAGGTGATGATGATGGCGATGATGACGACTACTTTGGTGMapped 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|5126497|gb|AI748233.1|AI748233EST: AGAAATCCAAACTCGATATGTCGCANAAGCNAACAAGGTCTAGCCCCGAG CTAGACATTGNGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGT
genomic: AGAAATCCAAACTCGATATGTCGCAAAAGCAAACAAGGTCTAGCCCCGAGgtaacattaa ... ttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgttgttagtatttgcctatttggaaattcattttcatgcttttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGACGATGACGATTACTTTGATG
cttttgttt CT-rich tract
aaattcattttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaagtttgcccaatggcatcgtgtagcccatgtagctgacttcacttgttgttagtatttgcctatttggaaattcattttcatgcttttgtttgcagCTAGACATTGGGGGAGGTGGGGGAGATATCGGAAAGAAAATCAATCATGGTGGTGGTGATGGAGGTGATGATGATGGGGACGATGACGATTACTTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - tgcccaa
- - - - - - - - - - - - - - -ccatgta
- - - - - - - - - - - - - - - - - - gctgact
- - - - - - - - - - - - - - - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgccta