Sequence
atgc intronic sequence ATGC exonic sequencegtctctaaattctgtggtttatttcaaaatatattatagttaaataaaaaaatgagactactaagcatgttgtggttgaaccaaatgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
Basic information
species | Glycine max |
transcript | GLYMA06G17140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 1
--gtctctaaattctgtggtttatttcaaaatatattatagttaaataaaaaaatgagactactaagcatgttgtggttgaaccaaa----------tgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
| | || | || | ||| | | | | | | | || | ||||| | || | | |||||| || ||| |||||||||||||| ||||||| ||||||| || |||||||||||||||||||||| | |||||||| ||||| |||| || | |||||
ttatattataacttcatgactggttttcttggaatctgcttatcagttttatgaagatagtactatg--tgcttctactcaaccaagatcattgacctgcagGAAGTGCTGGTGATGTGCTAGAAGACAATCCAGTTGGGCGGTTGAAGGTTTTTGTTTATGACTTGCCAAGCAAGTATAACAAGAGGATAGTCGCCAAGGA
upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G023020_T01 (Zea mays), 3'ss of exon 1
----------gtctcta---aattctgtggtttatttcaaaatatattatagttaaataaaaaaat-gagactactaagcatgttgtggttgaaccaaatgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
|||| | ||| | | | || | | ||||| | | | | | | | ||| | | | | ||| |||||| |||||||||||||| ||||||||| |||| ||||| ||||||||||| || ||||||| | ||||| || || || ||||| || | |||||
atgtagaaaaatctccatatgattgttttgctttgtctacttcatattttgttcatgtgtgttgcttgtgtggactgaaacagcaattatgaaac----tgtagGGAGTGCTGGTGATGTGTTAGAAGATAATCCTGTGGGTAGGTTGAAGGTCTTCATTTATGACTTACCAAGGAAGTACAACAAGAAGATGGTCACCAAGGA
upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 1
gtctctaaattctgtggt-ttatttcaaaatatattatagttaaataaa-----------aaaatgagactactaagcatgttgtggttgaaccaaatgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
| ||| | || || |||| | | | ||| || || || | | ||| ||| ||||| |||||||||| ||| || ||||||||||| ||||||||||| || || || ||| | ||||| | ||| ||||| || || |||||||| || ||||| | || | |||||
-tgcctagctagcgtaccgttccttcaggagaactcttagctaggtatgttcttttccccaattttatgctagccctaatgctgtggc-gaaccaaatgcagGAAGCGCTGGTGATGTGTTAGAAGATGACCCTGTTGGGAGGCTCAAGGTCTATGTCTATGATCTCCCCAGCAAATACAACAAGAAGCTGCTCAAGAAGGA
upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
------gtctct-aaattctgtggtttattt-caaaatatattatagttaa--ataaaaaaatgagactactaagcatgttgtggttgaaccaaatgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
||| | | ||||||| || | | || | | || | | | | || || | | || | || | || | | ||||||||||||||||||| || ||||||||||| |||||||| |||| || ||||||||||| |||||||| ||||| || ||||| || || || |||||
agcattatctttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 1
-gtctct--aaattctgtggttta------tttcaaaatatattatagttaaataaaaaaatgagactactaagcatgttgtgg-ttgaaccaaatgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
||| | ||| |||| |||| || | | | | ||||||| | || |||| || | ||| ||| ||| |||||||||| |||||||| || || ||||| ||||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||| ||||||||||||||
tgtcctttaaaaatctgctagcagcaaaattttcctaacctgtcaactgaacttaaaaaattaggatctctaaccacgccttgggttgcacctcatgtagGTAGCGCTGGTGACGTCTTGGAAGACAATCCAGTGGGAAGGTTGAAAGTTTTTGTTTATGAACTTCCAAGTAAATACAACAAGAAGATTCTGCAAAAGGA
upper sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 1
-------gtctctaaattctgtggtttatttcaaaatatattatagttaaa----taaaaaaatgagactactaagcatgttgtggttgaaccaaatgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
|| |||||| | | | || | | | | || | | || | | || | || ||| |||| | |||| ||| |||||||||||||| || |||||||||||||| |||||||||||||||||||| || || |||||||||||||| || || || || || || |||||
cccgagagttaaacaattctaagttctcttgagcagtttgatttaatggggactctgaagcatgtaatctgatctccactttg-ggtttcaatgaatgcagGAAGTGCTGGTGATGTTTTGGAAGATGATCCAGTAGGAAGGTTGAAGGTTTTTGTGTACGAGCTTCCAAGCAAATACAACAAAAAGATCCTTCAGAAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagttaaataaaaaaatgagactactaagcatgttgtggttgaaccaaatgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
taaataaaaaaatgag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctctaaattctgtggtttatttcaaaatatattatagttaaataaaaaaatgagactactaagcatgttgtggttgaaccaaatgtagGTAGTGCTGGTGATGTATTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA