Sequence
atgc intronic sequence ATGC exonic sequencegttatttatattctgacttacaaaaaactcagtgatttatctgtttataggttttaagttctatcactcaatcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
Basic information
species | Glycine max |
transcript | GLYMA02G07940.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 2
gttatttatattctgacttac---aaaaaactc----agtgatttatctgtttataggttttaagttctatcactcaatcatatgtctttggc-ttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
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-ctcttagtatttaagactatctgaaaacacttccaaaataaagtatat-tgtgtacggttgcagcaagtacttgcaatgactagtctttcatattattcagGTTGATCCTGATGAGGTCAATGCGTTGGCACAACTAATGACATGGAAGACGGCCGTGGCTAATATTCCATATGGAGGAGCTAAAGGTGGAATAGGATGCA
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
gttatttatattctgacttacaaaaaactcagtgatttatctgtttataggttttaagttctatcactcaatcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG----------------------------------------------------
| ||| || | || | | || || | ||||||| || |||||||| ||||| ||||||||| | ||||| ||||| ||||||||||| || ||||||||||| ||||||||||| || || || |||
----------------------------------------------gttggtgaaaaatctggtcctgatgtttgaaatcctttgacaacccaggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G178415_T02 (Zea mays), 3'ss of exon 3
------------gttatttatattctgacttacaaaaaactcagtgatttatctgtttataggttttaagttctatcactcaatcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
||| || ||| | | || ||||| ||| ||| ||| | || | || | | || || | ||||||| || |||||||| ||||| ||||||||| | ||||| ||||| ||||||||||| || ||||||||||| ||||||||||| || || || |||
atccatttccttcaaattaattttcctcttcatttaagactcattgaa--atccgttggtgaa----aaatctggtcctgatgtttgaaatcctttgacaacccagGTTGATCCTGATGAAGTTAATGCCTTGGCACAATTGATGACTTGGAAAACAGCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTA
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
gttatttatattctgacttacaaaaaactcagtgatttatctgtt-tataggttttaagttctatcactcaatcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
||| || || |||| || | | | | | | ||| || | |||| || || || || | |||||||||| |||||||| || |||||||| ||||| ||||||||||| |||||||| || || ||||| ||||| |||||||||||||| || || ||||
gtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattggcatgaagta---------aaccagatttcggtaatc--gacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 2
------gttatttatattctgacttacaaaa----aactca---gtgatttatctgtttataggtt---ttaagttctatcactcaa-tcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
| ||| | | |||| | || |||||| || | | | || || | || || | | ||| | ||| | | || || ||| | ||||||| || ||||||||||| || ||||| || || ||||||||||| |||||||| || || || || || || ||||| ||||||||||| || ||||
gtttttgaccttttgactttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttctt--gcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 4
--gttatttatattctgacttacaaaaaactcagtgatttatctgtttataggttttaagttctatcactcaatcatatgtctttg----gcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
||| || | ||| | ||| | | || | || ||| | | | | | | | | |||| ||||||||| |||||||| || ||||||||||||||||||||||| ||||||||||||||||| ||||| ||||| ||||| ||||||||||||||||| |||
ccagggttttcatgtagctttaaattaaatctactctccagcttgggaacagatttgtgctattgcagtttcagtttggatgatcgcatagcttttgtagGTTGACCCAGATGAGGTAAATGCTTTGGCACAACTAATGACGTGGAAGACAGCAGTAGCAAATATTCCATACGGTGGGGCCAAAGGAGGGATAGGATGTA
upper sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S62_236V6.3 (Physcomitrella patens), 3'ss of exon 3
---------gttatttatattctgacttacaaaaaactcagtgatttatctgtttataggttt----taagttct-atcactcaatcatatgtcttt-ggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
| ||| | | | | | | | | | || | || || || | |||| | |||| | ||| ||| | ||| | ||||||| |||| ||||||||||||||||| | ||||||||||| | ||||| ||||| |||||||| || ||||| || ||||| || || |||
gtatcttcaagtgtttgcaattagcgtaatgcacattcctttcatcgaaggtttggctggcttcctttgagttttcggtcttcaacaaaatgcgtttcgacttttgcagGTTGAGTTGAATGAGGTGAATGCTTTGGCACAGTTGATGACATGGAAATCTGCAGTGGCGAACATACCATACGGGGGAGCGAAGGGAGGCATTGGATGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtttataggttttaagttctatcactcaatcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
ttttaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatttatattctgacttacaaaaaactcagtgatttatctgtttataggttttaagttctatcactcaatcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG