Sequence
atgc intronic sequence ATGC exonic sequencegtaattctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
Basic information
species | Glycine max |
transcript | GLYMA02G42560.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
gtaattctttcatttggaaaaaaaaacttgtt-tttctgttggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
| | | | ||| || | ||| | |||| | ||| | || | || | ||| | || || || |||||||||||||| |||||||| || || ||||| || ||||| || | |||||| || ||||| || ||||| ||||| || || ||||| || || ||||||
----------------------gtagttaactactcctgatgttgatatgtgcgaagcaattttgtcctta----acgtggcgcacctta-atatcgttcttta-----cattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gtaattctttcatttggaaaaaaaaacttgtt-tttctgttggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
| | | ||| || | ||| | |||| | ||| | || | || | ||| | || || || |||||||||||||| |||||||| || || ||||| || ||||| || | |||||| || ||||| || ||||| ||||| || || ||||| || || ||||||
----------------------gtagttaactacacctgatgttgatatgtgcgaagcaattttgtcctta----acgtggcgcacctta-atatcgttcttta-----cattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
gtaatt-ctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgta-tttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
||| || || | | | | | || ||||| ||| | |||| | | ||| | ||| ||| | | |||| | | ||| ||| | | ||||||||||| ||||| || || || ||||| || ||||| |||| ||||| || ||||| || ||||||||||| || ||||| || ||||||||||||
gtagttactcttactcctgatg-----ttggtatttcttaaggtggcataccttaat--attaa---atttctcaacatggcatgcattgatattaaattttctttatattc----atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
| | | |||| || | | | | |||| | | | || | |||| || | || || | | ||||| |||| | || | |||||||||||||| || || || ||||||||||| ||||| || |||||||||||||| ||||||||||||||||| || ||||| || || |||||||||
-----------gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattctt----gtattt----atatgcttatgtttaca-atgtttctctc-----tgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
|||||| | ||| | | || | | | || || | | ||| | | | ||| | ||| || |||| | | ||||| | ||| ||||||||||||| |||||||| |||||||| || ||||| || |||||||||||||| |||||||||||||||||||| ||||| || || || ||||||
gtaattttatca---------agatcctgctgtcattcctgtaaacaagcaccatgcagc--aatttgtatt---tttatgacttacaatgtct-tccctctgtgtgata-------gTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 20
gtaattctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
|||||| || | | || || ||||| ||||| | ||| || || || |||| || |||| || | || || | | ||||||||||||||||||||| |||||||| ||||| ||||| || || || || ||||| ||||| |||||||||||||||||||| |||||||||| |||||||||
gtaatttgtttagt---aaggaagaactttgctttctttaggtgcggtac---atccaac-------ttattttgtgattttc-----atatcgttttcttttggtt-catggaacagTGAGGATCCTGACATTCACTTCAAGTATATTGAAGCTGCTGCTAAAACTGGACAAATTAAGGAGGTTGAGCGTGTGACTCGAGAATCAAACTTCTATGAT
upper sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
------------------------gtaattctttcatttggaaaaaaaaacttgtttt----tctgtt----ggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataa----------tatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
| | ||| ||| || || ||| || |||| | ||||| | || | |||| | ||| | || ||| ||| | ||| | | ||| | || ||| ||||| ||||| || |||| |||||||||||||| || ||||||||||| ||||||||||| || || ||||| |||||||| || || |||||| |
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgc--atgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCTMapped 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|207821924|gb|GD796869.1|GD796869EST: AGGTCATATGAAGGACTGTACTTTTTCCTTGGATCATACTTGAGCTCCAG TGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGG
genomic: AGGTCATATGAAGGACTGTACTTTTTCCTTGGATCATACTTGAGCTCCAGgtaattcttt ... tatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGG
EST:
gi|209720996|gb|BW682475.1|BW682475EST: TGTACTTTTTCCTTGGATCATACTTGAGCTCCAG TGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGG
genomic: TGTACTTTTTCCTTGGATCATACTTGAGCTCCAGgtaattcttt ... tatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
ctctaaa putative branch site (score: 3)
taaataatatggaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA