Sequence
atgc intronic sequence ATGC exonic sequence...gtattatgacgatgataatgagagttaagttttggtacagattgccatatatagttatgcagtattatgttctaatatctaattgatctttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA
Basic information
species | Glycine max |
transcript | GLYMA14G21410.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 3'ss of exon 5
-----------------------gtattatgacgatgataatgagagttaagttttggta---cagattgccatatatagttatgcagtattatgttctaatatctaattgatctttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA
||||| | | | | | | ||| | | || | || | | |||| || | | || | || || || | | ||||||||||||||||| |||||||||||||||||| | || ||| | ||||| || || |||||||||| |||
gtattgcagtttttgaaattttcttattacaatggatgtgtatactactgaactttagcatttcaaaaaagaattgaaacatatgtttccatacaaatttggtaatgatcatttttatttcaccagCCTAGCAGAAATTCAGAATGCACGAGGCATCATGGATGTTCTTTCCGAGATGTTGAATGCTTTGGATCCTAGTAACAGAGAG----
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 5
-gtattatgacgatgata-atgagagttaagttttggtac--agattgccatatatagttatgcagtattatgttctaatatctaattgatct-ttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA
| || | | | | ||| | | ||| || | ||||| | | || | | || || | | ||||| | |||| || |||||||| ||||| ||||||||||| || |||||||||||||| |||| ||| | ||||| | || ||| | |||| |||
ggccttgtcaagcaactgcatgtaattccctctttaatattaaagttgccttttcta---aggaaggtataaatcacattatcttgt--atctactccccaccagTTTGACAGAAATCCAGAATGCACGTGGTGTCATGGATGTTCTTTCAGAGATGTTGAATGCTATTGATCCTGGCAACAGAGAG----
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G053925_T02 (Zea mays), 3'ss of exon 5
--gtattatgacgatgataatgagagttaagttttggtacagattgccatatatagttatgcagtattatgttctaatatctaattgatctttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA--------------
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ttatatttatttcatgttttagatgtttgtgaacttgctgttgtcattggtttagcctatccagcatacaagtttggtaa-tgattg-cggtaatttaccagCCTTACAGAAATTCAGAACGCACGTGGCATCATGGATGTTCTTTCAGAGATGCTGGATGCTTTAGATCCAGGTAACAGAGAGGTACTTTCCTGATGCACC
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 5
--gtattatgacgatgataatgagagttaagttttggtacagattgccatatatagttatgcagtattatgttctaatatctaattgatctttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA
|||| ||| | || || | | | | | ||| ||| || | | || | |||| | ||| || | || ||||||||||| ||||| |||||||||||||||||| |||| ||||| |||| ||||| || |||||| |||
ttatatttatttcatgttttagatgtttgtgaacttgctgttgtcattggtttagcctatccagcatacaagtttggtaa-tgattg-cggtaatttaccagCCTTACAGAAATTCAGAACGCACGTGGCATCATGGATGTTCTTTCAGAGATGCTGGATGCTTTAGATCCAGGTAACAGAGAG----
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 5
---gtattatgacgatgataatgag-agttaagttttggtacagattgccatatatagttatgcagtattatgttctaatatctaattgatctttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA
|| | | | || | |||| || | || ||| | | | || | | || || | |||| | || ||| || || || ||||| ||||||||||||||||| || |||||||||||||| |||| ||| | ||||| | || ||| |||||| |||
gttataatttaatcattgttatgattagctgtgtcttgtt-tatttgatgattttccttcataaaggaa---gttcccaaataatgttgcctttctattgccagCTTGACAGAAATTCAGAATGCACGTGGGGTCATGGATGTTCTTTCAGAGATGTTAAATGCTATCGATCCTGGTAACAGAGAG----
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 5
gtattatgacgatgataatgagagttaagttttggtacagattgccatatatagttatgcag--tattatgt---tctaatatctaattgatct-ttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA
| | | ||||| | | || | || | || || |||| ||||||| ||| | | ||||| | | ||| || ||||||||| ||||||||||||||||| || || |||||||| |||||||||||||| | ||| ||||| || | ||||||||
------taaaatctgtctctctggttaacatcttttattgcatggtttcgatctttttgcaagttattatgcatgtcttgtttttaatttgtatattccttcctagTTTGACAGAAATTCAGAATGCACGAGGTATTATGGATGTCCTTGCAGAAATGCTGAGTGCATTAGATCCAGGAAACAAAGAG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatatagttatgcagtattatgttctaatatctaattgatctttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA
ttgatctttctttt CT-rich tract
taatatctaattgatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattatgacgatgataatgagagttaagttttggtacagattgccatatatagttatgcagtattatgttctaatatctaattgatctttcttttatagTTTGACTGAAATTCAGAATGCACGGGGCATCATGGATGTTCTTGCAGAAATGCTCAATGCCTTAGACCCTAGTAACAAAGAAGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - tgccata
- - - - - - - - - - - - - - - - - - - - - - - - - - -gttatgc