Sequence
atgc intronic sequence ATGC exonic sequence...gttaaaaagtgtgtaactgacttttctcgataagtaaattagtaaaatacagaggacttctcactgagaaaaccatttttttgtttatgactttatgtagCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
Basic information
species | Glycine max |
transcript | GLYMA11G36000.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 1
gttaaaaagtgtgtaactgacttttctcgataagtaaattagtaaaatacagagg-----acttctcactgagaaa-accatttttttgtttatgact-ttatgtagCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
||| ||||| || | |||| | | | ||| || | || ||| | ||| || ||| ||| || | || | |||| ||||||||||| || |||||||| ||||| | |||||||||||| | | | || || ||| || | || || || || | || || || ||||
-----aaaaaaaaaaactg--ttatactagtaagaatcatggcgaaaggcatgtgtttctgtttttcattttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 1
lower sequence: AT4G39660.1 (Arabidopsis thaliana), 3'ss of exon 1
gttaaaaagtgtgtaactgacttttctcga-taagtaaattagtaaaatacagaggacttctcactgagaaaaccattttt--ttgttta----tgactttatgt---agCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
| | | | || || |||| ||| || | | ||| | | || ||| | || | | || || | ||| |||||| |||| ||||| || || || |||||||| || | | ||||||| ||||||||| ||||| ||||| |||||||||||||| ||| | || || || || |
---------cgattcattagctcccgaagactaagaggatttgtggact-tagaagccagcttgatgatccatggatctctgattattcagtgttgatgttatgttgcagCTTAACATCGTTGAAGGGAAGATGCAGTACTTGTATGATGAGAGTGGTAGGCGATATCTGGATGCCTTTGCTGGAATAGTCACTGTGTCGTGCGGTCACT
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 1
---gttaaaaagtgtgt-aactgacttttctcgataagtaaattagtaaaatacagaggacttctcactgagaaaaccatttttttgtttatgactttatgtagCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
| || | | | | ||| ||||| | |||| | ||||| | || || | | | | | || || | | || || |||| |||| || || |||||||| ||| | || ||||||||||| | ||| ||||||||||| |||||||||||||||||| | || ||||| ||||
atcataaactaatatatgaacagacttgatgtactcagtacacctaataaatatcat---cccaacattgcatacatgttctaacttttcatta-tgtacacagGTCAATGTTGTTGAAGGGAAGATGCAGTATTTGTTTGATGAGAATGGCAAGCGCTATCTTGATGCCTTTGCTGGAATAGTTACTGTGTCATGTGGGCATT
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 1
lower sequence: EDO96807 (Chlamydomonas reinhardtii), 3'ss of exon 1
----gttaaaaagtgtgtaactgacttttctcgataagtaaattagtaaaatacagag------gacttc-tcactgagaaaaccatttttt----------tgtttatg-actttatgtagC---TCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
|| | | |||| | | || ||| ||| || | |||| || || | ||||| | |||| | |||||| ||| ||| |||||||||||||||||||||||| |||||||||| || || | || || || ||
gtaagtggtgggacgagaccctgatctggagctgcttgtggatttccaaaccctagcgatcgctgactcggtcgctcttgtccctattttatctcgcagCGCTGTTCTGGCACTTTAAAAAGCCTGTCATGATTGTGGAGGGCAAGATGCAATATTTATTCGATGAAAAGGGGCGACGCTACCTCGAC-------------------------------------
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 1
lower sequence: EFJ12384 (Selaginella moellendorffii), 3'ss of exon 1
gttaaaaagtgtgtaactgacttttctcgataagtaaattagtaaaatacagaggacttctcactgagaaaaccatttttttgtttatgactttatgtagCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
| ||| | | | || | | || | || | | | | || ||||||| |||||||| || |||||||||||||| | |||||||| ||| | | | || | ||||| |||||||| || || ||| | ||| || ||||
-------------------------------------gtgagtgtgaatttgtgtctttttgatggatgga--------ttgatcgcgggcgtcttgcagCTCAATATTGTGGAAGGGAAGATGCAATATCTTTACGATGAGAGTGGAAAGAGGTACTTGGATGCGTTTGCTGGGATTGTCACTGTTTCCGTGGGTCATT
upper sequence: GLYMA11G36000.3 (Glycine max), 3'ss of exon 1
lower sequence: EFJ33785 (Selaginella moellendorffii), 3'ss of exon 1
gttaaaaagtgtgtaactgacttttctcgataagtaaattagtaaaatacagaggacttctcactgagaaaaccatttttttgtttatgactttatgtagCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
| ||| | | | | ||| | | || | | || | | | || ||||||| |||||||| || |||||||||||||| | |||||||| ||| | | | || | ||||| |||||||| || || ||| | ||| || ||||
-------------------------------------gtgagtgagaatttgtgtccttttgatggatcgatcgatcgc--------gggcgtcttgcagCTCAATATTGTGGAAGGGAAGATGCAATATCTTTACGATGAGAGTGGAAAGAGGTACTTGGATGCGTTTGCTGGGATTGTCACTGTTTCCGTGGGTCATTMapped 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|151410465|gb|EV280280.1|EV280280EST: AACGGAAAAAGTTCCTTGGTCCTTCCTTGTTCCACTTCTATCAAAAACCT CTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGG
genomic: AACGGAAAAAGTTCCTTGGTCCTTCCTTGTTCCACTTCTATCAAAAACCTgtgagtctcc ... ctttatgtagCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatacagaggacttctcactgagaaaaccatttttttgtttatgactttatgtagCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
ttctcac putative branch site (score: 2)
atttttttgtttatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaaaaagtgtgtaactgacttttctcgataagtaaattagtaaaatacagaggacttctcactgagaaaaccatttttttgtttatgactttatgtagCTCAACATTGTGGAGGGCAAGATGCAATATCTATTCGATGAGAATGGTAGGCGTTATCTTGATGCTTTTGCTGGAATAGTTACTATCTCCTGTGGACATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA