Sequence
atgc intronic sequence ATGC exonic sequence...gtcaaatacaagtctctaaattctgtgatttatttcaaaatatattatagttaaataaaaaatgacactactaagcatgttctggttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
Basic information
species | Glycine max |
transcript | GLYMA04G37920.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 1
gtcaaatacaagtctctaaattctgtgatttatttcaaaatatattatagttaaataaaaaatgacactactaagcatgttctggttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
| | || || | | | | | | || || ||| | | || | | | | | | | | | | | || ||| ||||||||||||||| ||||||| ||||||| || |||||||||||||||||||||| | |||||||| ||||| |||| || | |||||
ttatattataacttcatgactggttttcttggaatctgcttatcagttttatgaagatagtactatgtgcttctactcaaccaagatcattgacctgcagGAAGTGCTGGTGATGTGCTAGAAGACAATCCAGTTGGGCGGTTGAAGGTTTTTGTTTATGACTTGCCAAGCAAGTATAACAAGAGGATAGTCGCCAAGGA
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 1
----gtcaaatacaagtctctaaattctgtgatttatttcaaaatatattatagttaaataaaaaatgacact-actaagcatgttctggttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
| || || | | ||||| | || ||| | | || || ||| || | | || | || || ||| ||| |||||| ||| ||||||||||||||||| |||||||| || || || ||| | ||||| | ||| ||||| || |||||||| || || ||||| | ||| | |||||
gctatgcttctaaaatttagaatattcttttccctaattctgtgcaaggtcta--tagatactccatagcttttgctta--atattgtggc-gaaacaaatgcagGAAGTGCTGGTGATGTGTTGGAAGATGACCCTGTTGGGAGGCTTAAGGTCTATGTCTATGATCTCCCAAGCAAGTACAACAAGAAGCTGCTGAAGAAGGA
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G023020_T01 (Zea mays), 3'ss of exon 1
gtcaaatacaagtctctaaattctgtgatttatttcaaaatatattatagttaaataaaaaatgacactactaagca-tgttctggt--tgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
| | || |||| | || | || ||| || || | ||| || | | || || | | | || | | | || |||||| |||||||||||||||||||||||| |||| ||||| ||||||||||| || ||||||| | ||||| || || || ||||| || | |||||
-atgtagaaaaatctccatatgat-tgttttgctttgtc-tacttcatattttgttcatgtgtgttgcttgtgtggactgaaacagcaattatgaaactgtagGGAGTGCTGGTGATGTGTTAGAAGATAATCCTGTGGGTAGGTTGAAGGTCTTCATTTATGACTTACCAAGGAAGTACAACAAGAAGATGGTCACCAAGGA
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 1
-gtcaaatacaagtctctaaattctgtgatttatttcaaaatatattatagttaaataaaaaatgacactactaagcatgttctggttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
| | | || | | || | | | | | || || | | ||| ||| | ||| |||||||||| ||| || ||||||||||||||||||||||| || || || ||| | ||||| | ||| ||||| || || |||||||| || ||||| | || | |||||
tgcctagctagcgtaccgttccttcaggagaactcttagctaggtatgttcttttccccaattttatgctagccctaatgctgtggc-gaaccaaatgcagGAAGCGCTGGTGATGTGTTAGAAGATGACCCTGTTGGGAGGCTCAAGGTCTATGTCTATGATCTCCCCAGCAAATACAACAAGAAGCTGCTCAAGAAGGA
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcaaatacaagtctctaaattctgtgatttattt-caaaatatattatagttaa--ataaaaaatgacactac-taagcatgttctggttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
| | | | | |||||||||| | | || | | || | | | | || || | | | || | || | || | | |||||||||||||||||||||| ||||||||||| |||||||| |||| || ||||||||||| |||||||| ||||| || ||||| || || || |||||
----agcattatctttcaggttctgtgattgagctacatagttaatccttgcttatgatgtgaactttaagtgtgtatctgtttttttcttctctgatgtttagGTAGTGCTGGTGATGTGTTGGAAGATGATCCCGTGGGAAGACTGAAAGTCTTTGTTTATGAGCTTCCAAGTAAATACAACAAGAAGATACTTCAGAAGGA
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 1
-gtcaaatacaagtctctaaattctgtgatttatttcaaaatat--attatagttaaataaaaaatgacactactaagcatgttctgg-ttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
||| || || ||| | |||| | || | | | | | ||| ||||| | | |||| || | ||| ||| ||| |||||||||| |||||||| || || ||||| ||||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||| ||||||||||||||
tgtcctttaaaaatctgctagcagcaaaattt-tcctaacctgtcaactgaactta---aaaaattaggatctctaaccacgccttgggttgcacctcatgtagGTAGCGCTGGTGACGTCTTGGAAGACAATCCAGTGGGAAGGTTGAAAGTTTTTGTTTATGAACTTCCAAGTAAATACAACAAGAAGATTCTGCAAAAGGA
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 1
---gtcaaatacaagtctctaaattctgtgatttatttcaaaatatattatagttaaataaaaaatgacactactaagcatgttctggttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
| | || | ||||| |||| | | || | || || | | | | | || | || || |||| | |||| ||| |||||||||||||| || |||||||||||||| |||||||||||||||||||| || || |||||||||||||| || || || || || || |||||
cccgagagttaaacaattctaagttctcttgagcagtttgattta-atggggactctgaagcatgtaat-ctgatctccac-tttgggtttcaatgaatgcagGAAGTGCTGGTGATGTTTTGGAAGATGATCCAGTAGGAAGGTTGAAGGTTTTTGTGTACGAGCTTCCAAGCAAATACAACAAAAAGATCCTTCAGAAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatagttaaataaaaaatgacactactaagcatgttctggttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
ttaaataaaaaatgac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaaatacaagtctctaaattctgtgatttatttcaaaatatattatagttaaataaaaaatgacactactaagcatgttctggttgaaccaaatgtagGTAGTGCTGGTGATGTGTTAGAAGATGATCCAGTGGGAAGGTTGAAGGTTTTTGTTTATGAACTTCCAAGCAAATATAATAAGAAAATTCTGCAAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - aatacaag
- - - - - - - - - - ttctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acactac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggttg