Sequence
atgc intronic sequence ATGC exonic sequencegttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
Basic information
species | Glycine max |
transcript | GLYMA04G09070.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatataca-tattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
|| |||| | | | ||||| |||| | | | || | | ||||| || | | | || | ||| || | | | ||| || | || |||||||||||| ||||| |||||||| ||||| || || ||||| |||||||| |||| || || || ||||||||||| ||||
-------------gagaagccattcacagcgcaa---acacttgggtgtcttgtaatgtttactgttggtatttattatgagcaagaagccaag--aactg-acttgaatg---cttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGC
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
| ||| | ||| | | | | || | | | | || || ||| || | || || | | | ||| ||| | | ||| || || || |||||||| || ||||| || || || || || || |||||||| ||||||||||||| || || |||||||| |||||||||||
----------gtcaagctgcgatt----gcaagcttttagctggaggctgtgacagtttatggtattgcacttgt-------agatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
| | | | ||| | | || | || || || | | ||| | | |||| | | ||| ||| || || | ||| || || || ||||| ||||| ||||| |||||| | ||||| || || ||||| |||||||| |||| || || || |||||||||||||||||
------------ggaaaatgagctactcaatccccgggaatcccagaggg----gatttaagtttccaaactagccctaaataaacaag-taatgactctggtttt--ctgttc--tccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
| ||| ||| || ||| | || | | | ||||| | |||| | | | | || | ||||| ||| ||| |||||||| ||||| |||||||| |||||||||||||| ||||| || |||||||| || ||||| ||||| ||||| |||||||| || | |||||
----------------------gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgtt--ttatctctgtttcacagttttcatc--atttgtatt--------cagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
| | || | ||||||| | || | | | |||| | | | || ||| | ||| | |||| ||||| | |||||| || ||||| || || || || ||||| |||||||| ||||| || |||||||| || ||||||||||| || || || |||||||| |||||||
-------------------------gtta-gtctaacatatttggc-------tgatggat-ttctatgacaaaatttatctatatt--ttgcttgacttcatttc-attgactcc---agGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCAAGTGGATAAATAAAAAATGGAGGGAGGGTTTCTATGTCACCTCTATGGC
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
gttaatacccctgaagtttttattcttcat-gtattgtgtatttggggtggcaataatatacata-ttttgactggttatgtttaaattgtcttctta-cttgtatttggattg-atccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
| |||| || | | || || || | || || |||||| | || || | ||| || | || || | | |||| | | ||| || || |||||| || || ||||| ||||| || |||||||||||||||||||| || |||||| ||||||| || || || || |||||||
------------------------cgtcatagtcctttttaattttagttattttttaatttttagttttgagttatt-cgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------------------gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
||| || | | | ||| || || || | || | || | | | | | | ||| | | ||||| | |||| | | | | | || || | |||| || |||| ||||| || || ||||| || || || |||||||||||||||||||| || |||||| ||||||| ||||| || ||| | |||||
gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgat-ctcaagggtgtttgatgatttat-tcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
|| | | | || | ||| | | |||||| || || || ||| || ||| || | ||| || ||||| || ||||| || ||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| || ||| | |||||
----------------------------------------------------gtattgtcgctgttattgatggcca--ctggcattgtcg-ctgacgcgtgttt-------cccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC
upper sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgttta--aattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
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-------------------------------------------------------------gtattgtcgctgttattgatggccactggcattgttgctgacgcgtgattc---ccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGCMapped 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|193616008|gb|FK569670.1|FK569670EST: GCCGGGGCTAATAATGGATCCTCATTGGTTGTAATGTCTAAAG GTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTA
genomic: GCCGGGGCTAATAATGGATCCTCATTGGTTGTAATGTCTAAAGgttaataccc ... atccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
tcctttt CT-rich tract
ttatgtttaaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA