Sequence
atgc intronic sequence ATGC exonic sequence...tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
Basic information
species | Glycine max |
transcript | GLYMA02G07800.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g20880.1 (Oryza sativa), 3'ss of exon 2
tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
|| || ||| || |||| | | || | ||| || ||| || | || | || |||| | | || ||||| ||||||||||||||||| |||||||| ||| ||||||| ||| | |||||||||||||| |||||||| |||||||| || |||||||||| || |||||||
-gt-tagtttctctttacatgctt-------tacacatttgttattatat--gttgatct------------taatctgttatgatgtttttttgtgtagGTTGAAAATCAAGAAGGTGTTGCTAATGTTGATGAGATAATTGCAAATTCAGATGCTTTCATGGTTGCAAGAGGAGATTTGGGAATGGAGATCCCAATTG
upper sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g16960.1 (Oryza sativa), 3'ss of exon 2
tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttgg----ttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
|| | | | || | | ||| || | || || |||| | || | | ||| | ||||||| ||||||||||| || || || |||||||| || |||||| | || ||||| || ||||| ||||| ||||| |||||||||||||||| || |
------------------------------gtataacattctcttttgagt-attgcacttctaagctgcactttgcaaagattttaatctattgaattttcagGTTGAGAATCAAGAGGGAGTGGCTAACTTTGATGATATCCTGGCACAATCTGATGCTTTTATGGTTGCAAGGGGTGATTTGGGAATGGAAATTCCGATAG
upper sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G003883_T01 (Zea mays), 3'ss of exon 2
tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
| | | | | | | | | | | | | | | || | |||| |||| || || ||||||| ||||||||||| || || || |||||||| || |||||||| || ||||| || ||||||||||||||||| | |||||||||||||| || |
----------------gtatggttctagcattttcttttgggtttcaaactagtagattttcaaattcaaggttata-attgttttg--aacatg--cagGTTGAGAATCAAGAGGGAGTAGCTAACTTTGATGATATCCTGGCAAACTCTGATGCTTTTATGGTGGCAAGAGGTGATTTAGGAATGGAAATTCCTATAG
upper sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G26390.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
||| | | || | | || | ||| ||| | | || ||| || | || ||| | | || |||| | ||| | | || |||||||||| ||||| ||||| || ||||||||||| || || ||| || ||||| || ||| | |||||||||||||| |||||||| ||||||||||
-gtacatat---atacatacatcactcaaactaat--ataaatcacatatccata-----ctcagattcttatgatatgtta--cttttgatattgtcagGTTGAAAACCAAGAAGGTGTAGCGAATTTTGATGATATCTTGATAAACTCGGATGCGTTTATGATCGCAAGAGGTGACCTTGGAATGGAGATTCCAATTG
upper sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g07600.t01 (Vitis vinifera), 3'ss of exon 2
tgtataagttccctatacaagtctatgaaaataagaaacagttct--tgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
|| | | | | ||| | ||| || | | || | | | | | | || || ||||| ||||||||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| |||||||| || |||||||| ||||||||||| || ||||
--------------------gtatgttgaggttgcaaagaactctgttgaagtatttgcatttttgggaaggatatgactaat---tttgtgatttggc-agGTTGAAAATCAAGAGGGTGTTGCTAATTTTGATGAAATTCTTGCAAACTCAGATGCATTTATGGTGGCCAGGGGTGACCTTGGAATGGAAATCCCCATTG
upper sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S124_70V6.2 (Physcomitrella patens), 3'ss of exon 3
tgtataagttccctat---acaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
| | || ||| ||| || || ||| || | | | | | |||| | | | ||||||| | | || || | | | |||||||| ||||| || ||| | | || || ||||| ||| || | | |||| | | |||||||||||||||| |||||||||||||| ||||| | |
-ggttttactcagtatgagacaggttta--aaattatgtgattctgcctctattcaaagaatcacaaaattgtgtcttgatcctgctttgatttctaccatagGTTGAGAATCAGGAAGGTCTGGTGAACTTCGATGACATATTGAAAGAGACAGACGGAGTCATGGTGGCAAGAGGGGACCTGGGAATGGAGATTCCTACGG
upper sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S90_133V6.1 (Physcomitrella patens), 3'ss of exon 3
-----tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
|| ||| || ||| ||| || | | ||| | ||| | | | | |||| | || ||| | | | ||||||| || || || ||| | | ||| || || || ||| || | | || |||| | |||||||||| |||||||||||||| ||||| ||||||| |
cttattgcggaagatct-tatcgaagcct-tagctgcatttcacactgaaaatatcaacacatc-cgtttgttgtgggtgttgtttgaatcg--gatcaatgcagGTTGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAGAGAGTCGGATGGAGTCATGGTGGCTAGAGGTGACCTGGGTATGGAGATTCCAACAG
upper sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S90_134V6.1 (Physcomitrella patens), 3'ss of exon 3
-tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttc-ttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
||| || || || | | || | | | |||| | | || | | ||| || ||| || ||||| |||| || || || || ||| | | ||| || || || ||| || | | | |||| | |||||||||| |||||||||||||| ||||| ||||||| |
ttgtgcaaaatcaacattccgaccaatctcttgtcgtgatatttctgaaaccgtagaaaaattaacaatgtgtcccaaccctgccttaattattttga--agGTCGAGAACCAGGAAGGTCTGGTCAACTTCGACGATATATTGAAAGAGACGGATGGAGTCATGGTGGCCAGAGGTGACCTGGGTATGGAGATTCCAACAGMapped 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|298197652|gb|HO045131.1|HO045131EST: AGGAAAGCCTGCAAAAAGCATACTTCTCATGTCCAAG GTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCA
genomic: AGGAAAGCATGCAAAAAGCATACTTCTCATGTCCAAGgtatccatcc ... ttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
gattaac putative branch site (score: 2)
ttgtcttcttgtttt putative PPT
aaattgtacttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtataagttccctatacaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - gtctatg
- - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - gttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccca