Sequence
atgc intronic sequence ATGC exonic sequencegtttgtaatatcaaattgacacatccaaaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
Basic information
species | Glycine max |
transcript | GLYMA17G05410.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 7
--------gtttgtaatatcaaattgacacatccaaaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
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gtacaactattttgactatttcacatctggtcttcacatatacaacacagttcttgaatgt-aatgatacttctttcatt-cttcagGTTTTACAGCGCATTTTAATGGGTACTGATGTTGTTAAAAACGTCAACAAGAATAATGCCTCACATGCTGTTCTCTTTGAAGCTCTTGCTCTT
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 7
-----gtttgtaatatcaaattgacacatccaaaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
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gtactaccttttcttttaacttttctagtgcacctgtacaaaaatgtgtgg---actgcaatgattttgttgttgtc-cttcagGTTTTACAGCGTATTTTGATGGGTACTGATGTTGTTAAAAATGTTAACAAGAACAATGCCTCACATGCTGTTCTCTTTGAAGCTCTTGCTCTG
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 8
gtttgtaatatcaaattg-acacatcca--aaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
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----gtactacctttttttacttctctactgaacctgtactaaaatgtgtggattataatgatattattgtcatc-cttcagGTTTTACAGCGCATTTTGATGGGTACTGATGTTGTTAAAAACGTTAACAAGAACAATGCCTCACATGCTGTTCTCTTTGAAGCTCTTGCTCTG
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
gtttg-taatatcaaattgacacatccaaaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
||| || | ||| | | | | || | | | || | | || || | |||||||||| | || | ||| |||||||||| |||||||| ||||||||||| ||||| ||||| || ||||| || || ||||||||||| | |||
gttcaatattttcatgtgtaaatctgtaatatatgtctttgaatttcctctcatggcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGGACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCTGTGCTGTTTGAAGCTCTATCCCTG
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 7
gtttgtaatatcaaattgacacatccaaaaaaaaaaaa-atagttaacaaattttagtga--gccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
|| |||||| | | ||| | | | || | |||| | | | || || | |||||||||| | || | ||| ||||||| || |||||||| ||||||||||| ||||| ||||| || |||||||| || ||||||||||| | |||
-------gta-caaattttcttgtgtaaatatctgatatatgtcttcgaaatctctctcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 7
gtttgtaatatcaaattgacacatccaaaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcattt-cagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
|| || || | || | || || | || |||| || ||| || | | ||| ||||| ||||| ||||| | ||||| ||||||||||| ||||| |||||||| || ||||| || ||||| ||||| |||||||| ||||||||
gtactccatttctcagcga-atatatttcaattctcatcagattttgtaattctaatgaaatctgttgggtggttttcagGTTCTACAACGGATATTAATGGGAACTGATGTTGTGAAAAACGTGAACAAGAACAATGCCTCACATGCTGTTCTGTTTGAAGCCCTTGCTCTT
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------gtttgtaatatcaaattgacacatccaaaaaaaaaaaaatagttaaca-aattttagtgagcct--tgattaatcattt----------cagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
|| | || | || | | || ||| | | || |||| | | ||||| | || ||||| ||||||||||| || |||| || ||||||||||||||||| ||||||||||||||||| ||||| ||||| || || |||||||| ||
gtaagctgatacttatgtctattctttttttctatttcattccctaaattgcttctgtttctcgtacactgttcttatggttctctcggtcataaggagcgtattaattaactaatttttttgggtacagGTTTTACAAAGGATCTTGTTGGGCACGGATGTTGTAAAAAATGTCAACAAAAATAATGCATCTCATGCTGTTCTCTTCGAGGCTCTTGCGTTG
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------gtttgtaat-atcaaattgacacatccaaaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
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cactatttacatccaaatgtattgaattactgaggatcctattgatgtttccatactta----tccttttatccttttctattgcgacgtg-ttacgttttgtagACTTTGCAGCGCATTTTGTTGGGAACTGATGTTGTAAAGAATGTCAATAAAAACAATGCCTCGCATGCGGTACTCTTTGAAGCACTCGCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaaaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
gattaat putative branch site (score: 3)
tcatttc CT-rich tract
aaaaaaaaaatagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtaatatcaaattgacacatccaaaaaaaaaaaaatagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC