Sequence
atgc intronic sequence ATGC exonic sequencegtaagctcaaagctgtaaaaaataacgtcaaatgatggtaaattttgctatacttttatgacatggatcaatgatacttattgcggtcttcttctggatcaatacttaatttcaataatctgatttttaaatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAACCTTCAAGAA
Basic information
species | Glycine max |
transcript | GLYMA10G00830.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaagctcaaagctgtaaaaaataacgtcaaatgatggtaaattttgctatacttttatgacatggatcaatgatacttattgcggtcttcttctggatcaatacttaatttcaataatctgattttta--aatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAACCTTCAAGAA
| || || | ||| | | || | || || || || || ||| |||| |||| | |||||||||||||||||| || |||| || || | | | |||||||||||||| ||||||||||||||||||||||| ||||||| ||||| ||||||||
-----------------------------------------------------------gtcagtgaagcagaatatatgatttagttctagctcccattgttattttgttctaaacgtctttttttctccaatgtgatacagAGATATCAAGCCTGATAATCTGCTACTTGACAAAGACGGCCACATGAAATTGTCAGATTTTGGATTATGTAAACCATTAGACTGTAGTAATCTTCAAGAG
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagctcaaagctgtaaaaaataacgtcaaatgatggtaaattttgctatacttttatgacatggatcaatgatacttattgcggtcttcttctggatcaatacttaatttcaataatctgatttttaaatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAACCTTCAAGAA
| | | | | | | || || || || | || |||| | | | || || | || | ||| || |||||||||||||||||| || |||| || || |||| || |||||||| ||||| ||||||||||||||||| || |||| || |||| || || |||
-----------------------------------------gtctagtgaagcaatcaactatctgagtaa--atttgtagcgtatcatttttcttttttggtgttctgac-catccatttacttctccaatttgttacagAGATATCAAGCCTGATAATCTGCTACTCGACAGAAGCGGTCACATGAAGTTATCCGATTTTGGATTATGTAAGCCATTAGATTGTAGTATTCTCCAGGAA
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 4
gtaagctcaaagctgtaaaaaataacgtcaaatgatggtaaattttgctatacttttatgacatggatcaatgatacttattgcggtcttcttctggatcaatacttaattt-caataatctgatttttaaatgc--attccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAACCTTCAAGAA
| || | ||||| || || |||| ||| || ||| ||| ||||| ||||| |||||| |||||| | | || | | ||| ||||||||||||||| ||||| || ||||| |||||| |||| || |||||||| ||||||||||||||||||||||| | || |||||||| ||||| ||
------------------------------gtttgtgtaagattttatcatgattgtatg---tggg--aaccata-----tgcatgcttct----gatcatgacttaagaagcaataaccctctccatatttacttattacagAGATATCAAGCCCGACAATTTACTGCTCGATAGATATGGACATATGAAATTGTCAGATTTTGGATTATGTAAACCATTGGATTGCAGTAATCTTCATGAG
upper sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagctcaaagctgtaaaaaataacgtcaaatgatggtaaattttgctatacttttatgacatggatcaatga-tacttattgcggtcttcttctggatcaatacttaatttcaataatctgatttttaaatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAACCTTCAAGAA
| | || ||| | | | | ||| | ||||| | | | | || | | ||| | ||| | || || | ||||||||||||| || |||||||||||| |||||| ||||| |||||||| ||||| |||||||| | ||||| || | |||||| ||| | | |
-------------------------------------gcttggtatgaaggactctctcg-tgttcactgatgcctgtttatttgaaattgatgttccgcttacttttgactccaaca-tctactggtt---tgtgtaccagAGATATCAAACCGGACAACTTGCTGTTAGATAAGAATGGGCACATGAAGTTATCTGATTTTGGCCTCTGTAAGCCTTTGGACTGCTCCAACTTGCCTGCCMapped 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|254348922|gb|GR852601.1|GR852601EST: GAGACTGTCCTAGCCATAGAGTCAATTCATAAACATAATTATATTCATAG AGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATT
genomic: GAGACTGTCCTAGCCATAGAGTCAATTCATAAACATAATTATATTCATAGgtaagctcaa ... tgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATT
EST:
gi|31561374|gb|CD487212.1|CD487212EST: GAGACTGTCCTAGCCATAGAGTCAATTCATAAACATAATTATATTCATAG AGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATT
genomic: GAGACTGTCCTAGCCATAGAGTCAATTCATAAACATAATTATATTCATAGgtaagctcaa ... tgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcttctggatcaatacttaatttcaataatctgatttttaaatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAACCTTCAAGAA
atctgat putative branch site (score: 4)
atcaatacttaatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctcaaagctgtaaaaaataacgtcaaatgatggtaaattttgctatacttttatgacatggatcaatgatacttattgcggtcttcttctggatcaatacttaatttcaataatctgatttttaaatgcattccagAGATATCAAGCCTGACAACTTGCTGCTAGATAGAAATGGCCACATGAAATTATCAGATTTTGGATTATGTAAACCGCTAGACTGCAGTAACCTTCAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG