Sequence
atgc intronic sequence ATGC exonic sequenceggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtggttgggaagatgttaattggagctgtgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG
Basic information
species | Glycine max |
transcript | GLYMA17G37820.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 5
----------ggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtggttgggaagat----------gttaattggagctgt-----gttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG-
|| | | | | | ||| | | |||| || | | | | ||||| ||||| || |||| || | |||| ||||| || |||||||| | | || || |||||||| ||||| |||||||| || |||||||||||||| || | || ||||||||||| ||||
gtactgccttttcatctttccagctgattactgcactcacaatatttgtttatt-tataataataaagattatcctctcaaataatttgaactgtttgatatttttgcagCTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCTGTGTACTTGGTTGCTGACTATGTTGAAGT
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 5
--------------------------------------------------ggtatgtatgttgtggcacattgctgaa--gtagtttttgcttgtaatgtggttgggaa-gatgttaattgga-gctgtgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG-
|||| || | || ||| | || || | || | | | || || || || | ||||| || | || | |||| ||||| || |||||||| | | || || |||||||| ||||| |||||||| || ||||||||||| || || | || ||||||||||||||||
gtattgttttttcatctgtcaggctgatttgtgcaatccaatatttgtttaatatg-ataatctgaatatttgtttaatattactgttctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGTTTGGTGTTGGCTTCTACTCGGTGTACTTGGTTGCTGACTATGTCGAAGT
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 5
----ggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtggttgggaagatgttaattggagctgtgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG-
| || ||||| ||| || ||| | | | | | || || | || || | |||| ||||||||||| |||||| ||||||| ||| | || || ||||| || |||||||| || |||||||||| ||||| || |||||||| | ||||
gtacgttacttatgtggtgatacgttgtc----ctgcataatagtatggatcaataaattccatatttctaagatcttgcctttcgcagCTTTTGTTGAGAAAATGCAATCAAGTGGGGATTTGAACCTTATTGGACAATTTGGAGTTGGATTCTACTCTGCCTATCTTGTTGCTGACTACATTGAAGT
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 5
--------ggtatgtatgttgtggcacattg--ctgaagtagtttttg---cttgtaatgtggttgggaa---gatgttaattggagctgtgtta-attcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG-
| || | | | | ||| ||||| | || || ||| | | | | || |||||| | | || || ||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||| || |||||||| || ||||||||||| ||||| || || |||||||| ||||
gtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttcttttatatagCTTTTGTGGAGAAAATGCAAACCAGTGGGGATCTTAATCTCATTGGACAATTTGGAGTTGGGTTCTACTCTGTATATCTTGTTGCAGACTATGTTGAAGTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|208261680|gb|GE060035.1|GE060035EST: AGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCT GCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTG
genomic: AGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtatgtatg ... tgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTG
EST:
gi|298170585|gb|HO019209.1|HO019209EST: AGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCT GCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCCGATTGGGCAG
genomic: AGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtatgtatg ... tgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtttttgcttgtaatgtggttgggaagatgttaattggagctgtgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG
tgttaat putative branch site (score: 3)
atgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtggttgggaagatgttaattggagctgtgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAGTTTGGAGTCGGCTTCTACTCTGTTTATCTCGTGGCTGACTATGTCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG