Sequence
atgc intronic sequence ATGC exonic sequence...agcaattgagtgagaaaaatagagctctgatttgttataagttttactccataaagattaattcaaaattcatcaatatttttttcttgttcatttgcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTT
Basic information
species | Glycine max |
transcript | GLYMA04G32130.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G32130.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g41310.1 (Oryza sativa), 3'ss of exon 1
---agcaattgagtgagaaaaatagagctctgatttgttataagttttactccataaagat-taattcaaaattcatcaatatttttttcttgttcatt-tgcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTT
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atgcatgattaaccatcaaagat-gagatgtgccctacca-aaacgttcttcaatctggatgtatcactaaattc--tgac-ttgtttcttgatacattatgcagAGGCATACGATCCGCTTGATCCAAATGGGAACATAACAATCAAGTGGGATGTGCTGCAATGGACTCCAGATGGATATGTT
upper sequence: GLYMA04G32130.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
agcaattgagtgagaaaaatagagctctgat-ttgttataagttttac-tccataaagattaattcaaaattcatcaatatttttttcttgttcatttgcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTT
| | | | || || | | | ||| || | || | ||| | ||| | | |||| | | ||||||||||| |||||| ||||||||||| || || || ||||| ||||||||||| || |||||||| || ||||||||||||
--ctacaaaccaaataattagtagttttaagattgaagcaatcacaatgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
upper sequence: GLYMA04G32130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 1
--agcaattgagtgagaaaaatagagctctgatttgttataagttttactccataaagattaattcaaaattcatcaatatttttttc-ttgttcatttgcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTT
| | | | | || | | | |||| | || ||| |||| ||| || ||| | | ||| |||| || || ||| |||||||||||||| | || ||||| | |||||||| || |||||||||||| | || |||||||| |||||||||||||||
aatgttttctaat-atctctattgtgtgtcagtgaaatatatatatttctcagaaaagg--gattgaagatttagccttatcttttgggtttctccttttcagAAGCCTATGATGCACTGGATCCCAATGGAAATATCACGATCAAATGGGATATTATGAGCTGGACTCCAGATGGCTATGTT
upper sequence: GLYMA04G32130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
agcaattgagtgagaaaaatagagctctgatttgttataagttttactccataaagattaattcaaaatt----catcaatatttttttcttgttcattt--gcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTT
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-ccaa--aaaaagaaaagattgaactctccctttatg-aaatttaatgtcatgagaatc--ttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTMapped 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|192300281|gb|FG988788.1|FG988788EST: AGCAGTCTTGCTCCTGTTACTGTTTTCTTTCTCCACTTTCTCTTCTACAG AAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATG
genomic: AGCAGTCTTGCTCCTGTTACTGTTTTCTTTCTCCACTTTCTCTTCTACAGgtattggctg ... tcatttgcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATG
EST:
gi|192308403|gb|FK002803.1|FK002803EST: AGCAGTCTTGCTCCTGTTACTGTTTTCTTTCTCCACTTTCTCTTCTACAG AAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATG
genomic: AGCAGTCTTGCTCCTGTTACTGTTTTCTTTCTCCACTTTCTCTTCTACAGgtattggctg ... tcatttgcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actccataaagattaattcaaaattcatcaatatttttttcttgttcatttgcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTT
gattaat putative branch site (score: 3)
tttttttcttgttcat putative PPT
ataaagattaattcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcaattgagtgagaaaaatagagctctgatttgttataagttttactccataaagattaattcaaaattcatcaatatttttttcttgttcatttgcagAAGCCTATGATCCGCTTGATCCAACCGGAAATATAACAATCAAATGGGATGTCATTAGCTGGACCCCAGATGGCTATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - tgagtga
- - - - - - - aaaaata
- - - - - - - - - - - - - -tgatttg