Sequence
atgc intronic sequence ATGC exonic sequencegtaccctgtcattggtctatgcaggctctcttttatttctgtctccacttcatagctgactaattcagtggactgacattttttattgtgcaattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
Basic information
species | Glycine max |
transcript | GLYMA03G33910.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 7
------------------gtaccctgtcattggtctatgcaggctctcttttatttctgtctcc-----acttcatagctgac-taattcagtggactgacattttttattgtg-caattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
| || | | || ||| | || | | | ||| ||||| | ||| || | | | |||| | || || | ||| | | | || | | | |||||| ||||| || |||||||| |||||||| ||||||||||| ||||| || |||||||| || || |||||||||||||||||||||| |||||||
gtaataaaaatgagtcttgaactgtttattttgtcagtccat-cattgtgttagcactgtccactacttactgtgcagtttatgtgtttcatttgattg-cttttctcacaataataaggtcattgattgtagTTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAG
upper sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 7
gtaccctgtcattggtctatgcaggctctcttttatttctgtctccacttcatagctgactaattcagtggactgacatt-ttttattg--tgcaattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
| || | || || | | | | ||||||| | ||| | | | | ||| | | || | || | |||| || || || || || || || |||||||| |||||||| || || || |||||||| || ||||| ||||||||||||||||| || || ||||||
---------tgcggcactgt-tagactttttcatcgagttcatcaaacttcattcatt-ttaaatggggaaatggttattgtcctgatgaatatggcgttgttgtcgacagTGGAGAAAGCAAAATACATCTACATTGCTGGCTTTTTCCTTACGGTCTCCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAG
upper sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 7
gtaccctgtcattggtctat--gcaggctctcttttatttctgtctccacttcatagctgactaattcagtggactgacattttttattgtgcaattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
| |||| ||| || || || | ||| || ||| | || ||| | | | || | |||||| | ||| || | ||||||| ||||| || || || || |||||||| ||||||||||| || ||||| ||||| |||||| ||||||||||||||||||| ||||||||||||
-tgtgttgtccttgactgatcgatagcctttatttgatctctatttct-cttaagacgtactggttttctttagctgacag--------atataatattcttgatgccagTTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG
upper sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 7
gtaccctgtcattggtctatgcaggctctcttttatttctgtctccacttcatagctgactaattcagtggactgacattttttattg-tgcaattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
| ||||| || | | || || | ||| | | | || || || | || || | | | | | | | ||| || | ||||||||||||| || || || || |||||||| |||||||| || || || || ||||| ||||||||||| |||||||||||||| ||||||||||||
-------tttattggccttaactga-tcgattatctttatttgctctctatttatcttaa-gatgcaatagttttctttacctgacaaatataatattcttgatgacagTTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAG
upper sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G089767_T01 (Zea mays), 3'ss of exon 5
gtaccctgtcattggtctatgcaggctctcttttatttctgtctccacttcatagct--gactaattcagtggactgacattttttattgtgcaattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
| | | |||| || || | ||| | |||| || | | | || | || | || | | | |||| || | | |||||| ||||| || |||||||| |||||||| |||||||| || ||||| || ||||| || || || |||||||||||||| ||||||| |||||||
--------atgtggtttcttgcatatcatcattgctgcttgtttgcactcaatgcttttgtatcatggattgtgtttactgactatgatatgcacgcattaattat--agTTGAGAAGGCAAAATATATTTACATTGCTGGATTTTTCCTTACGGTATCCCCGGATTCTATTCAACTTGTTGCTGAGCATGCCGCTGCAACTAACAAG
upper sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 7
gtaccctgtcattggtctatgcaggctctcttt-tatttctgtctccacttcatagctgactaattcagtggactgacattttttattgtgcaattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
|| | | || |||| | |||| | | || | ||| |||| || ||| | ||||| || || | | | |||||||||||||||| ||| | ||||||||||| |||||||| ||||| || || || || || | || || ||||| ||||| |||||||| || |||
--------------gtat-tattttctttcttgatgcttctattccttgtttgttgctatataatatgctgaactttcttttttattta---aactcctattttgacagTTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG
upper sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 7
gtaccctgtcattggtctatgcaggctctcttt-tatttctgtctccacttcatagctgactaattcagtggactgacattttttattgtgcaattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
|| | | || |||| | |||| | | || | ||| ||| || ||| | ||||| || || | | | |||||||||||||||| ||| | ||||||||||| |||||||| ||||| || || || || || | || || ||||| ||||| |||||||| || |||
--------------gtat-tattttctttcttgatgcttctattccttgtttgttgctatataacatgttgaactttcttttttattta---aactcctattttgacagTTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGMapped 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|193359917|gb|FK324239.1|FK324239EST: AAATTGCTACAAATCTGATCATTTGAAGAGACCAGAAAATTGGGCACTAG TTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCAC
genomic: AAATTGCTACAAATCTGATCATTTGAAGAGACCAGAAAATTGGGCACTAGgtaccctgtc ... tctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCAC
EST:
gi|6482402|gb|AW201663.1|AW201663EST: AAATTGCTACAAATCTGATCATTTGAAGAGACCAGAAAATTGGGCACTAG TTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCAC
genomic: AAATTGCTACAAATCTGATCATTTGAAGAGACCAGAAAATTGGGCACTAGgtaccctgtc ... tctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctgactaattcagtggactgacattttttattgtgcaattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
ttctcac putative branch site (score: 2)
ttttttctcac CT-rich tract
attttttattgtgcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccctgtcattggtctatgcaggctctcttttatttctgtctccacttcatagctgactaattcagtggactgacattttttattgtgcaattttttctcacgcagTTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC