Sequence
atgc intronic sequence ATGC exonic sequence...ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
Basic information
species | Glycine max |
transcript | GLYMA07G18310.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 1
---ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatt-tccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | | |||| | || | | || | || || | | | ||| | |||| || | | ||| ||| | ||||||| | || || |||||||| |||||||||||||| |||||||| |||||||| ||| | || |||||||| |||||||| ||||||||||| || ||
ttttgtaagacacctcttcacatttccctgtgaaatgcctgtatgctatatatttaaatatataaaatgtttaatctgatcc----actatcttgattgttcagGTGAAAAATTTTCTGAAATTGTGGGAAGTCCATATTACATGGCTCCTGAAGTGCTGAAGAGAAACTATGGACCTGAAATAGACATATGGAGTGCTGGTGT
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 1
ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacag-tatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | || | | | | || | || ||| ||| ||||| | | || || | | || || | || || |||||||| ||| || |||||||| ||||| |||||||| |||||||| || || | ||| | || ||||| || ||||||||||| ||||||||||||||
-tggactcacagtgcttgtacaacagttgatcgttgttctttgtatacagacaaaactcctagttccatccagtccttatgtgattgttatgttcttttagGTGAGAAGTTTTCTGAAATTGTGGGAAGCCCATATTACATGGCTCCAGAGGTATTGAAGAGAAACTATGGTCCGGAAATAGATATTTGGAGTGCAGGAGT
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 1
ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | | | | | || | | |||| | | ||||| || | | | | | | |||| |||||| | ||| || |||||||| ||||||||||| || |||||||| ||||| | ||| |||| |||||||| |||||||| |||||||| || || ||
gcaaaggcttgcctcggttcccttcttcagaccccactcatgtggccgtcttcccactttatttatttgaaactcataaaagcattgttttcttttctagGTGAAAAGTTTTCGGAAATTGTGGGAAGTCCATACTACATGGCTCCTGAAGTCTTGAAGAGGAACTATGGACCTGAAATAGACATATGGAGCGCTGGTGT
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 1
---ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | | | | | | || | || | | | | | | | |||| | |||| | | || | | | | | |||||| | ||| ||||||||||| ||||| || ||||| |||||||| ||||| | ||| | || ||||| ||||||||||| ||||||||||| |||||
tagaacgttgctgattgcaatacttgcaggacaggcatgtgtactacaca-agtaaacccta-gttttatctggccttttctca-tcctttgttctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 1
--ctcatgtttcac-tttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
| | || | |||| ||| | || | ||| | || | | | | | | | || ||| || || || | || |||||||||| ||||| || |||||||| ||||||||||| ||||| || || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||
attgtaggatttatgtttcttgattg--atacatacctttgatgtattttgaccagtttatttggtgttgatgctgt-ttttgtaatgcttacatatgaccagGTGAGAAATTCTCTGAGATTGTTGGGAGTCCATATTACATGGCACCTGAGGTGCTTAAGCGGAATTATGGACCCGAAATAGATATTTGGAGTGCTGGAGT
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
ctcatgtttcactttcaaaattatatttcaatctttttcattgcttaca-gtatctgacatattttcc--ataatgtgttgtgggtaa-tataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
|| |||| || ||||| ||| ||| | | || | | | | || | | ||| | | | || ||| | || ||| ||||||||||||||| ||||||||||||||||| ||||| |||||||| || || |||||||||||||||||||||||||||||||||||||||||||||||
tagttgcaaggcttt----atcttatttaaataagtttgctaatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGTMapped 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|16277961|gb|BI942654.1|BI942654EST: TTCGCCGCTCAAGGCAATTGATTTTGGCCTCTCCATATTCTTCAAGCCAG GTGAGAAGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGGAG
genomic: TTCGCCGCTCAAGGCAATTGATTTTGGCCTCTCCATATTCTTCAAGCCAGgtacgctgaa ... aaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAG
EST:
gi|16277967|gb|BI942657.1|BI942657EST: TTCGCCGCTCAACGCAATTGATTTTGGCCTCTCCATATTCTTCAAGCCAG GTGAGAGGGTCTTAGAAATTGTT
genomic: TTCGCCGCTCAAGGCAATTGATTTTGGCCTCTCCATATTCTTCAAGCCAGgtacgctgaa ... aaatttccagGTGAGAGGTTCTCAGAAATTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
tttcc CT-rich tract
taatataaaaatttcc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT
-tcatgtt
- - - - -cactttc
- - - - - - - - - - - - - - - - - - - - -tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - tctgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg