Sequence
atgc intronic sequence ATGC exonic sequence...tgtcttatcctgagtagaacattacaagcatgatttttctacttatgatcccaactagttaccttcaaattgggatagaggctaagttctacatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
Basic information
species | Glycine max |
transcript | GLYMA03G29600.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g41900.1 (Oryza sativa), 3'ss of exon 5
tgtcttatcctgagtagaacattacaagcatgatttttctacttatgatcccaactagttaccttcaaattgggatagaggctaagtt----ctacattt-gcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
| | | | | |||| || || | |||| | || | | | ||| | || || | | | ||| | ||||| |||||| ||||||||||| ||||||||| | || || || ||| |||| || || ||||| |||||||||| ||||| ||
--acacagac-atgcgaagcatt-cagttatctatcttctgat-atagtacttagcggttttgattgcatgcagacatgctcaatgttgtgattgcattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGCTGGGCAAAGGATGAAAAGACATTGAAA
upper sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 3
--tgtcttatcctgagtagaacattacaagcatgatttttctacttatgatcccaactagttaccttcaaattgggatagaggctaagttctacatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
| | | | | || || | | ||| || | || | | | | | | | | | | | | | | | ||| ||||||||||||||||||||||||||||||| | ||||| || ||| ||||||| || |||||||||||||||| ||| |||||
tagagcctgtgttaactattaccctttcttc-tgacttctgtagtagatgttctggcacatgatttggcattctataaactgtttttgct-tacttttgcagGTCATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAGAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
upper sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G037104_T02 (Zea mays), 3'ss of exon 4
-----tgtcttatcctgagtagaacattacaagcatgatttttctacttatgatcccaactagttaccttcaaattgggatagaggctaagttctacatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
|| | |||| || | ||||| | | || | || | | | | | | || ||| | | | | || || ||||||||| ||||||||||||||||||||| | ||||| || ||| |||| || || |||||||||||||||| ||| |||||
tgaattgatagaacctgtgttaactattac---cctttcttctgtagtagatgttctggcacatgat-ttggtattctataaactgttttgctc-acttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
upper sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
tgtcttatcctgagtagaacattaca--agcatgatttttctacttatgatcccaactagttaccttcaaattgggat-agaggctaagttct---acatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
| || | | |||| || | || | | | ||||| | || | | | | | | || | ||| | |||||||| ||||||||||||||||| || |||||||| |||||||| |||| ||||||||||||||||||||| |||||
------tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttatctgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
upper sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 5
-tgtcttatcctgagtagaacattacaagcatgatttttctacttatgatcccaactagttaccttcaaattgggatagaggctaagttctacatttg--cagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
| | ||| || | || ||| ||| || | | | | || | | | ||||| | | || || |||| ||||| || || |||||||||||||||||||||||| | |||||||| |||| ||||||||||||||||||| | |||||
tagatgtcgtctgcatacatttttctttgca--attgctc-attgaacactttgacacctctatatatatacaggataaatgttatgtgtccaatttattcagGTGATAGGTTGGTCAATGTGGTTTTCTGAGTATTTATTTCTGGAAAGAAACTGGGCCAAGGATGAAAGCATAATAAAG
upper sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S72_209V6.1 (Physcomitrella patens), 3'ss of exon 4
----------tgtcttatcctgagtagaa---cattacaagcatga-tttttctacttatgatc-ccaactagttaccttcaaattggg----atagaggctaagttctacatttgcagGTCATTG-GCTGGTCAATGTGGTTTTCTGAGTATCTTTTT-CTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG------------------------------
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gttatttgtttcccttgtacccggtgaaaacccttggcaattgtgggcttttagggattcaatcgtctagggggtatgcgctgattatgttttgttggaactgaattgagtatttcttgggcgttgcagAGATTGGGGTGTCTAGGTGGGACTCGAGCTGTTATGAAGAAGTCCACCAAATTTCTTCCGGTCATTGGCTGGTCTATGTGGTTTTCAGAGTATGTGTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatcccaactagttaccttcaaattgggatagaggctaagttctacatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
ttcaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcttatcctgagtagaacattacaagcatgatttttctacttatgatcccaactagttaccttcaaattgggatagaggctaagttctacatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG