Sequence
atgc intronic sequence ATGC exonic sequencegtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
Basic information
species | Glycine max |
transcript | GLYMA02G13860.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
---------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
| || | | | || || | || | | | |||| | || ||| ||||| |||| ||||| ||||| |||||||||||||| ||||||| ||||| || ||||| |||||||||
gtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaaactgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG----------------------------------
upper sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g38080.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------------------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattg-gat------tttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
| | | | | || || | ||| | | | | || |||| | |||| | | |||| |||| |||| ||||| ||||| || |||||||||||| | || ||||||||||| ||||| ||||||||
gtataccctacatacaaaatttgaacagtttcaaatttttttaaatattttttttggggggaagagaacagtaatatttacaaatttcttcaaactgatcacctgaactatgagtcaaataattgaagattgtggtgttatgtttcttggcagCTGAGAAGGGAGAAGATCAGCGAGAGGATGAAGCTCCTGCAAGACCTTGTCCCTGGCTGCAGCAAA----------------------------------
upper sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G137541_T01 (Zea mays), 3'ss of exon 2
----------------gtaagattttgtga------gaacttatctgtgatgaagatga--agttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
|| ||||| | | |||| | | |||| || | | | | | |||| || ||| |||||| |||||||||| ||||| || |||||||||||| |||| || |||||||| ||||| ||||||||
gtacggatttggtcacccaacgttttgccgcttgctggatcgctctgaaactgacatgaccggtcctgaaaaccctggctgttgcattgcatcttccctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTTCTGCAGGACCTTGTTCCTGGTTGCAGCAAA----------------------------------
upper sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G818643_T01 (Zea mays), 3'ss of exon 2
------------------------------------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
| |||| |||| || | | | ||| | | | | ||||| |||||| |||||||||| ||||| || |||||||||||| | || || ||||| || ||||| ||||||||
gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgcggtctggaattcacaccccaatgttta-accctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAA----------------------------------
upper sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G818643_T02 (Zea mays), 3'ss of exon 2
------------------------------------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA-
| |||| |||| || | | | ||| | | | | ||||| |||||| |||||||||| ||||| || |||||||||||| | || || ||||| || ||||| |||||||| || | | ||| || | || | || |
gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgcggtctggaattcacaccccaatgttta-accctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGT-CTATCTTCCACACAGAAGAAAGAAAAGG
upper sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G68920.2 (Arabidopsis thaliana), 3'ss of exon 3
---------gtaagatt-ttgtgagaacttatctgtgat-gaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
||| | | | || | ||| | || |||| | || ||| || || | |||| || | |||| ||||| ||||| || ||||| |||||||||||||||||||| || ||||| || |||| ||||
gtacaatttctaaaactatcttggaagtttaagtcgaatagaagctatctcttcttgtatttttcatct--aattactttgcgatgatagGTTAGGAGAGAAAAAATTAGTGAAAGGATGAAGTTTCTTCAAGATCTAGTACCGGGTTGCAACAAG----------------------------------
upper sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0010g00740.t01 (Vitis vinifera), 3'ss of exon 3
gtaagattttgtgagaac----ttatctgtgatgaagatga----agttttttggatgaagaatttcaaat--tggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
|||||||||| | | ||| | |||| | | | | | | | || || | | |||| || | ||||| || ||||||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||||
gtaagatttttcatggatagttttagttttgatagaagcaattctattgtcctagtcttggagttaaagctggtggaccttgatgacagGTAAGAAGGGAAAAGATCAGTGAAAGGATGAAGTTTCTTCAAGACCTGGTACCTGGTTGCAGCAAG----------------------------------Mapped 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|193378765|gb|FK345106.1|FK345106EST: GTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGA GTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTCTCTTCAAGACCTTGTA
genomic: GTCAAGCAACAAATAGCCATAGCCTTGCAGAGAGAgtaagatttt ... ttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
ttttcact CT-rich tract
aagaatttcaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG