Sequence
atgc intronic sequence ATGC exonic sequencegtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
Basic information
species | Glycine max |
transcript | GLYMA19G43790.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
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------------------------acgaattactt-ggattcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaa---tgtgttaattttc--tgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 7
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
|| || || | || || || || ||| | || | | || || ||| | || | | | || ||| || | || | ||||| || ||||| ||||| || |||||||| || |||||||| || |||||||||||| |||| || ||||| ||||| || || || |||||||||| ||||
------------------------ccatttgttttgtgtggattacatttgt-tcactgttttctttatatagtcttaactgtgt-ataacgttta---ctgagttaataatcttggatcatgg-tgcagATATTTCTCATATGAACACTTTTATGTGATCTACTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
||| |||| | ||| || ||| || | || || |||| || || | |||| | || | | |||| | | || |||||||| ||||||||||| ||||| |||||||||||||| |||||||||||||| ||||| |||||| |||| |||||||| ||||| || ||||||
-----------------------------gtactgacaaaaacaaatttg-tgctattgttgta------tatatggtattgt-ttctgctcatttaacatgactt--ttctacttactttggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
|||||||| | | ||| | | || | ||| | | | ||| ||| || || |||| | ||||||||||| ||||| ||||| ||||| |||||||||||||| |||||| |||||||||||||||||||||| || |||||||||||||||||| |||||
----------------------------------------------gttggtgtcttaagattaattagtaatatgaaattggtgcttattaac--ggcttttattaagactctctactgtttatt--agGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 7
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
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------------------------------gtactgacaaaaatatttgcgtgctattgttgtatttatagtattgtttttgc-tcatttaacatcacttttctattcactttggcaat--------tagATACTTCTCGTATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGCGATAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
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-----------------tatcagtttgccc--tcacgaaaagtaattatgataccacgac----gtgagcttaa-gtttctg-atcatgtgcccttaggct-----aaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgcct-taatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
||| || | ||| | | ||| | || ||| | |||| | || ||| || | | || || || | || | | | | |||||||||||||| ||||| ||||||||||| ||||| ||||| || |||||||||||| ||||||| || || |||||||||||||| | || | |||||
--------------------tattggcat-gccctcaatagaagacagtatggta--cattgatgtgaatt---taggtttctacttgtgtatctgtaggctcatccacgt-----aatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 3'ss of exon 7
gtagatataattgaaaatgtcatt----tcaattaacttcagaaaatgaccttggtgtc---attattcaaatg---aactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
|| | | || | || || | || | | | ||| || |||| ||| |||| | ||| | | | | | ||| || || | ||| | | | || | | | |||||||| || || |||||||||||||| || ||||| |||||||| ||||| || ||| |||||||||| || || |||||||| || ||||| | |||||
gtcaactccgatcaacctttctttcacgttgtttgatcccctgacttgatttttttgtcgatatttttcattttctcaacagagtgcagct-ttttaccatcaattgagttttcaagattattttgaacgctgtgtgcagGTATTTTTCGTATGAGCATTTTTACGTCATATATTGCAAGTTCTGGGAACTAGATTCAGATCATGACTTTTTCATAGACAAGGATGATCTCCTTCGATAT
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
gtagatataattgaaaatgtcatttcaattaacttcagaaaatg-accttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
| | | | ||| || | ||| |||||| |||| | | | || | | ||| || | | || ||| | | ||| |||| || || || ||||| ||||| |||||||| |||||||||||||||||| |||| | ||||| || || |||| ||||| || | || | ||||
------------------------gcgaggga--tgagagcttggatctttttgtcat-attccagtttagtatgctaacaaagactataataattgacctttggatacatg----tggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
ccttaat putative branch site (score: 4)
ttaatctttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA