Sequence
atgc intronic sequence ATGC exonic sequencegtactactatatttattgtattttagtgtcaagaatctcataattaaatattttctcatcttatgccacatatataactaatggggatggtcatttgtatttggtaatagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCTGATATTAAAAGAGGGAAATTTTCCCAAGAAGAAGAACAAACAAT
Basic information
species | Glycine max |
transcript | GLYMA01G09280.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G09280.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g51799.1 (Oryza sativa), 3'ss of exon 1
------gtactactatatttattgtattttagtgtcaagaatctcataattaaatattttctcatcttatgccacatat--ataactaatggggatggtcatttgtatttggta------atagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCTGATATTAAAAGAGGGAAATTTTCCCAAGAAGAAGAACAAACAAT
|||| | | || | || | |||| || || || || | || | | | || | | ||| | || || | ||| || ||| || |||||||||||||| || || ||| |||| |||||||||||| ||||||| || || || ||||| || || || | || | | || ||
gtatgtgtacatgcacaacggatg-gcgtacgtagctttgatcttgtagctag-catcgatccaaatgcagctatagctcgatggcca-tggcgttgagttttccttttttttacatgttgcagGGCTGAACAGGTGTGGCAAGAGCTGCAGGCTAAGATGGACGAACTACCTGAGGCCAGACATCAAGAGAGGAAAGTTCACCTCTGCCGAGAAGGATACCAT
upper sequence: GLYMA01G09280.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G159547_T01 (Zea mays), 3'ss of exon 1
---------------gtactactatatttattgtattttagtgtcaagaatctcataattaaatattttctcatcttatgccacatatataactaatggggatggtcatttgtatttggtaatagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCTGATATTAAAAGAGGGAAATTTTCCCAAGAAGAAGAACAAACAAT
| || | | | ||| | | | || || || || | || | | | || || || || | | || || | ||| ||||||||||||||||| || || ||| | || ||||| |||||||||||||| || || || |||||||| || |||| || |||||||| || ||
gtacgtgactgccgggaacaaacctctccatt-tctctcggtctcggtgtgacgatgtaaaagaggtcgatcgcttccatgcgaaaatgtagctcatcgatctagttgtt--------attgcagGGCTCAACAGGTGTGGCAAGAGCTGCAGGCTGAGATGGACCAACTACTTGAGGCCAGACATCAAGAGAGGGAAGTTCACCCAGGAGGAAGAACAGACCAT
upper sequence: GLYMA01G09280.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g05670.t01 (Vitis vinifera), 3'ss of exon 1
gtactactatatttattgtattttagtgtcaagaatctcataattaaatattttctcatcttatgccacatatataactaatggggatggtcatttgtatttggtaatagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCTGATATTAAAAGAGGGAAATTTTCCCAAGAAGAAGAACAAACAAT
| ||| || || | || | |||| | ||||| ||| || ||| || | | | | || || || | ||| || ||||| ||||| || || |||||||| || |||||||| || || |||||||||||||||||||| |||||||| |||||||||||||| |||||
----------gtctatgttaattaattgg-atccctctccctgtctctcattttttcag--tacttcac-catttcatcatt--------tcccttttactc--ctgcagGTCTTAACAGATGTGGAAAGAGCTGTAGGTTGAGATGGACGAATTATTTAAGGCCTGATATTAAAAGAGGAAAATTTTCTCAAGAAGAAGAACAGACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatcttatgccacatatataactaatggggatggtcatttgtatttggtaatagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCTGATATTAAAAGAGGGAAATTTTCCCAAGAAGAAGAACAAACAAT
aactaat putative branch site (score: 2)
acatatataactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactactatatttattgtattttagtgtcaagaatctcataattaaatattttctcatcttatgccacatatataactaatggggatggtcatttgtatttggtaatagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCTGATATTAAAAGAGGGAAATTTTCCCAAGAAGAAGAACAAACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC