Sequence
atgc intronic sequence ATGC exonic sequence...ttgttaaagaaatatggtcaagctagatcttaattagtttatggtttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
Basic information
species | Glycine max |
transcript | GLYMA16G24200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g38834.1 (Oryza sativa), 3'ss of exon 2
----------ttgttaaagaaatatggtcaagctagatcttaattagttt-atggtttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgc----agAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| | | | | |||| | || | | | ||| | || | | | || || ||||| || | || ||| ||| | | | |||| | |||||| |||||||||||||||| ||||||||| ||||| ||| |||| |||| ||| || || || ||||| || || ||||| || || ||
gtttaattaatcttcatacatatatacttaatttcatgcatgcatagctagatcaatcgagctagctatatatagatcgatgc-tgatcatgcatggattggggtgggtgagaagAGCATTGCAGGATAGGGTACGAGGAGCAGAGCGAGTGGTACTTCTTCAGCTACAAGGACAGGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGAT
upper sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G025642_T02 (Zea mays), 3'ss of exon 2
------ttgttaaa-gaaatatggtcaagctagatcttaattagtttatggtttttatttctt----ttaaatttggagatgc----atggttgtgaatgatttgagttttgcagAGACAT-ACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| | || | | | | ||| | || | | | | | | | | | | | | || | | | ||| || || | | | | | || | ||| | |||| |||||||||||||| ||||||||||| ||||| ||| |||| ||| || || || || ||||| | |||||| | ||||||||
gtacgctagctagccgcagctccggccagcctgttccgatccggcctgtcgatctgaactgctggcgatgatcttaaatttcctgctctggctggctctgctctcaatctctcaagGGCATTGCGGGATCGGGTACGAGGAGCAAAACGAGTGGTACTTCTTCAGCTACAAGGACCGCAAGTACCCCACGGGGACGCGGACCAACCGGGCCACCAT
upper sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgttaaagaaatatggtcaagctagatcttaattagtttatggt-ttttatttcttttaaa--tttggagatgcatggttgtgaatgatttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| || | | | | | | ||||| || |||| ||| ||| || | ||| ||| | | || |||| || | || || || ||||| || || || |||||||| ||||| ||||| ||||||||||||||||| ||||||||||| || ||||| |||||
---------------------gttacttaccgaacaccgtgagatattttactttggttaaggttttattgat-tatcaccttaaat--tttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
upper sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G66300.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgttaaagaaatatggtc-aagctagatcttaattagtttatggtttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
|| | ||| |||| | || | | | | | | | ||| | || | ||| || | || ||| || ||||| || ||||| |||||||||||||| | |||||||||||||| ||||| | ||||||||| ||||| |||||||| || || ||| |||||||| |
-aatttatgaattatgatttaaacgataccacctacacatgtaagcaactatactgtgtagctcgaaagagtaatatgtaacctaaatgtgatacgtgtagAGAGATGTAGGATAGGGTACGAGGAGCAAACGGAGTGGTATTTCTTCAGCCATAGAGACAAGAAGTATCCGACTGGGACTAGGACAAACCGAGCCACCGT
upper sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G36160.1 (Arabidopsis thaliana), 3'ss of exon 2
-ttgttaaagaa-atatggt-caagctagatcttaattagtttatggtttttatttctttta-aatttggagatgca----tggttgtgaatgatt-tgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
|| | | | || | ||| | || || || | | ||| | || || || | | | ||| || | | | || | | | ||| || | || ||||| | | | || || || ||||| || || ||||||||||| ||||||||||| |||||||||||||| || |||||||| |||||||| |||||
gttttcacaaaatacatgatgcatacttaatttaggat--ttttttcttcttcttaatctgacaatgtgaatacatagatctgatgagcattaattatgtatattatagAGAGCTGCCGAATCGGATATGAGGAAAGAAATGAATGGTATTTCTTCAGCCACAAAGATAAGAAATATCCAACAGGAACAAGAACAAACAGAGCGACCAT
upper sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
ttgttaaagaaat-atggtcaagcta----gatcttaattagtttatggtttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| ||| | || | ||| | | | || ||| || || | ||| || || | | || ||| ||| || | |||||| || | |||| ||||| || |||||||| |||||||||||||| |||||||| || |||||||||||||| ||||| || ||||| ||||| |||||
-ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttg---ttcaaagcgaataattg-atctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
upper sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------ttgttaaagaaatat-------ggtcaagctagatcttaattagtttatggtttttatttcttttaaatttggagatgc-----atggttgtgaatg-atttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| ||| || ||||| | | | || || | || | ||| | | | || | | || | | | ||| | || ||| | |||||| | || | |||| | |||| ||| ||||| ||||| |||||||| |||||||||||||| ||||| | | | ||| |
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGAC-GCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------
upper sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
------------ttgttaaagaaatatggtcaagctagatctta--attagtttatggtttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgcagAGACA------TACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| | ||| | | | | | || || || ||| | | | | | || | | |||| ||| |||| || | ||| | | | ||||| | || ||||||| |||||||||| ||||| |||||||||||||||||||| || || ||||| || |||||||||||||||
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
------------ttgttaaagaaatatggtcaagctagatcttaattagtttatgg---tttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgcagAGACA------TACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
| | ||| | | | | || | | ||| | ||| | | | | | || | | |||| ||| |||| || | ||| | | | ||||| | || ||||||| |||||||||| ||||| |||||||||||||||||||| || || ||||| || |||||||||||||||
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
tttcttttaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttaaagaaatatggtcaagctagatcttaattagtttatggtttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - -aaagaaa
- - - - - - - - - caagcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg