Sequence
atgc intronic sequence ATGC exonic sequence...tgaatccaacaggttttactcactgtgtgtagcaactggcaagtagcagcacatgtctgctctcaccctaaattttacatctgaatgttttgattggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG
Basic information
species | Glycine max |
transcript | GLYMA17G34950.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g26130.3 (Oryza sativa), 3'ss of exon 9
------------------------tgaatccaacaggttttactcactgtgtgtagcaactggcaagtag---cagcacatgtctgctctcaccctaaatt---ttacatctgaatgt--tttgattggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG
|| || | |||| | || | | | | || | ||| || | |||| ||| | || || ||| ||| |||||||||||||||||||| |||||||||||||||| || || ||||| |||||||| |||||||||||||| ||||
gtgtgttataatgtttatgctccacaaaatgggcatagtacactctccgtactctgaagtggtctggttgttccagttgataatgatgtgtaaataaaataatattaaaagcgattgctatttctttgttagCTTCTGGAACTTCGATGCACTGTTCCAGCCCCAACAGCATCCTGCTCGGGATTCACACGATACATTTTTTCTTGAAG
upper sequence: GLYMA17G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G101463_T01 (Zea mays), 3'ss of exon 9
tgaatccaacaggttttactcactgtgtgtagcaactggcaagtagcagcacatgtctgctctcaccctaaattttacatctgaatgttttga--ttggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG
| || | || | | | | | | | | | | | || | |||||| ||| | || | ||| |||||||||||| |||||||| |||| ||||| ||||| || || ||||| |||||||||||||||||||| ||| |||
-ggatttctgggccattgtaacatatagattata-ttactgctttctggattaagagtccctgcattcctaattttgcatgtttttgctgctgctttgccagCTTCTGGAATTTCGATGCACTGTTTCAGCCTCAACAGCATCCTGCTCGGGATTCACATGATACATTTTTCCTGAAAG
upper sequence: GLYMA17G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G39280.2 (Arabidopsis thaliana), 3'ss of exon 9
--------------tgaatccaacaggttttactcactgtgtgtagcaact---ggcaagtagcagcacatgtctgctctcaccctaaatt-------ttacatctgaatgttttgattggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG
| || |||||| | | || || | | | || |||| || ||| | | || | |||||| | | | |||||||||||| || ||||| ||||||||||| || || ||||| ||||||||||| ||||| || || ||||| |||
gtatcctctagttattaagaatcttggttttcagctttccatggaggctttaaggatatctaattatacat-ccttttcttgctatttgttggctgatcttaatctgattcatatacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG
upper sequence: GLYMA17G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv03s0063g02560.t01 (Vitis vinifera), 3'ss of exon 9
-tgaatccaacaggttttactcactgtgtgtagcaactggcaagtagcagcacatgtctgctctcaccctaaattttacatctgaatgttttgattggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG
|| || || ||| | | | | | | | | |||||| | | | | | ||| || | | |||||||||||| || ||||| |||||||||| ||||||||||| |||||||||||||||||||| || || ||| |||
atgcatttccagggctttgaatgttaacccactattttagtggtgaccgatatttttttgctcttagattttaatccctttatga-tgctccaccttccagCTTCTGGAATTTTGATGCACTGTTCCAGCCACAACAACACCCTGCTCGTGATTCACATGATACCTTCTTCCTGCAAG
upper sequence: GLYMA17G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S358_20V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------tgaatccaacaggttttactcac-tgtgtgtagcaactggcaagtagcagcacatgtctgctctcacc-----ctaaattttacatctgaatgtttt---gattggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG
| || | || | | | ||| || | | | | | || | || | | | ||| | | || |||| || | | ||||||||||| |||||||| |||||||||| ||||| || ||||| ||||| || ||||| || ||||| || | |
gtacttggaacgcatcaatcacctattttcttcttatttgcatttattcgaaactttcccttagattgcatgaaattaatacgcatgtttgagactgcaccctcttcggtacatgttgttgagttaagcgttttctagtactcatattgttttgttcgtgggaattgtagCTTCTGGAATTTCGATGCACTGTTCCAGCCTCAACAGCATCCAGCCCGTGACTCTCATGACACCTTTTTCTTGAAGG
upper sequence: GLYMA17G34950.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ30485 (Selaginella moellendorffii), 3'ss of exon 9
tgaatccaacaggttttactcactgtgtgtagcaactggcaagtagcagcacatgtctgctctcaccctaaattttacatctgaatgttttgattggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG
||| | | || | | | | | ||| | | ||| || | | ||||||||||| |||||||||||||||||||| || || || || || || || ||||| || ||||| || | ||
------------------------------------------gtacttgt-cttgacaacaattgcgtcgagtttaagcatt---tgtctttac-gatagCTTCTGGAATTTCGATGCCTTGTTCCAGCCGCAGCAGCATCCTGCCCGGGACTCACACGACACATTCTTCTTAAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagcacatgtctgctctcaccctaaattttacatctgaatgttttgattggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG
taaattttacatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaatccaacaggttttactcactgtgtgtagcaactggcaagtagcagcacatgtctgctctcaccctaaattttacatctgaatgttttgattggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - tccaaca
- - - - - - - - - ctcactg
- - - - - - - - - - - - - - - -gcaactg
- - - - - - - - - - - - - - - - - - - gcaagta
- - - - - - - - - - - - - - - - - - - - - - - cagcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctga