Sequence
atgc intronic sequence ATGC exonic sequence...gcaatgagcatcctccaacacatttaactgttcatcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
Basic information
| species | Glycine max |
| transcript | GLYMA17G17010.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 2
------gcaatgagcatcctc-caacacatttaactgttcatcaccctttttgtgttttgtgttttatgatttttct---ctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
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gtagtagctagcagcgccatagtgacagacacctctcgccaccatgccgccatggcttccaccttcacagcttcacttaacctcaagtaaaaaaaccttgtaaaaagcagGCATAGGTGGACTGGGAGATATGAGGCACACCTCTGGGACAACAGCTGCAAGAAGGAAGGCCAGACCAGAAAAGGACGCCAAG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 2
-gcaatgagcatcctccaacacatttaactgttcatcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
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tgtattgatgaggcacctactcttttgtttttgagcaaatcatttgaccctttttatattgaatgacgaaggtttgtgtgtgtttgat-tcactggagcagGCACAGGTGGACTGGAAGATATGAAGCCCACCTCTGGGATAACAGTTGCAAAAAGGATGGACAGACAAGGAAGGGAAGGCAAG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G146688_T01 (Zea mays), 3'ss of exon 2
----------gcaatgagcatcctccaacacatttaactgttcatcaccctttttgtgttttgtgtttta---tgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
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gtacgtacgtacacgccgccgtgtcgagctagttgactggtccgtccgcccgtccgtccatggagctgaagctgaagttgaaactaaaactaaaactgaaagtaattaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTGTGGGACAACAGCTGCAAGAAGGAAGGCCAGAGCAGGAAGGGCCGGCAAG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G021573_T02 (Zea mays), 3'ss of exon 1
gcaatgagcatcctccaacacatttaactgttc--atcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
| | |||| | |||||| | | | | || | | || | | || || | ||| | | | || | || | |||||| ||||||||||||||||| ||||| || || |||||||||||||||| ||| || ||||| | || ||||| |||||||
-tgtctgttagggccaaacagttcagactgtttgaaccgcgactgttttatactgaatgatg-gagggttttgtttgtgttggattggattcactggagcagGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
--gcaatgagcatcctccaacacatttaactgttc--atcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
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ctctgtctgttagggccaaacagttcagactgtttgaaccgcgactgttttatactgaatgatg-gagggttttgtttgtgttggattggattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G028151_T01 (Zea mays), 3'ss of exon 2
----------------------gcaatgagcatcctccaacacatttaactgttcatcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgt---atcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
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gtatcctcccaactcccgaccgtccgtacgccgtcgctgtcgcaggcgcgcgcgacccgcagcatccggcgcccgtgcgatcgagtcgctcactggccgcgtggtttcccaccgtgcaaaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTCTGGGACAACAGCTGCAGGAAGGAAGGGCAGACCCGGAAAGGCCGGCAAG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
gcaatgagcatcctccaacacatttaactgttcatcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
| | | || | | || | || | |||| ||| || | ||| | | | ||| | |||| ||| | |||| | ||| ||||| |||||||| ||||||||||||||||| |||||||| || | |||||| || || || || || |||||||||||||
--------gttgtttttttattttataatattaa--actttgtttgactttcgttagtaatgttacatatacttact--taaaaggt-tatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
upper sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 2
gcaatgagcatcctccaacacatttaactgttcatcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
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gtgtttttttccctcatgtttcccccttttgccttccttgttttcctatcacatctttaccttctttttttttttctttttcctgttttatgtctatcagGCATAGATGGACAGGTAGATATGAAGCTCATCTATGGGACAACAGTTGCAAGAAAGAAGGGCAAAGCAGGAAAGGAAGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
ttctaaa putative branch site (score: 2)
ttttatgatttttctc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaatgagcatcctccaacacatttaactgttcatcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
-caatgag
- - - - - tcctcca
- - - - - - - - - - - - - - - - - -caccctt
- - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgtt
