Sequence
atgc intronic sequence ATGC exonic sequence...aaaaattatttaattgtattaggattaactctactcatttatcttttactgtatttttggtttgagactctggccaactgttcctgttcacaattctcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
Basic information
species | Glycine max |
transcript | GLYMA12G28780.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G28780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G435034_T01 (Zea mays), 3'ss of exon 2
aaaaattatttaattgtattaggattaactctactcatttatcttttactgtatttttggtttgagactctggccaactgttcctgttcacaattctcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
| | ||| || ||| | | | || | |||| | | || | | || || || | | ||||||||||| | | ||||| || |||||| ||||||| | || |||||||| ||||||||||| ||||||||||| || || |||||||| | ||| ||
cttactaattgaactgtcagcttaccattttcaccgaattattctctgagttaaaatgtcatcactacaggacttaaagtttaattgcttggctcttcagGTTTATTAAAAAATTTGGCACTCATATAGTTGTTGGCCTAAAGATGGGTGGGAAAGATGTAATTTATTTGAAGCAACAACATTCATCAACCTTGCAAGCT
upper sequence: GLYMA12G28780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G028758_T01 (Zea mays), 3'ss of exon 2
--------aaaaattatttaattgtattaggattaactctactcatttatcttttactgtatttttggtttgagactctggccaactgttcctgttcacaattctcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
|| | || ||||||| || | || | | | || | || | ||| || ||| || || | | || ||| | || || ||||||||||||||| ||||| || || ||| |||| ||| | |||||||| || |||||||| ||||||||||| || || || || |||| | |||||
gtttctcagctaaatggtttattgtataagta--gacgttgcaaaggaatatactagt-tatattgcacctgaacctttg----attcttgctgctt-cacttttcagGTTTATTGATAAGTTTGGAACACACATAGTTGTCGGTGTAAAAATGGGAGGGAAAGATGTTATATATTTGAAACAACAACATTCGTCAAGCTTGCAACCA
upper sequence: GLYMA12G28780.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g01040.t01 (Vitis vinifera), 3'ss of exon 3
aaaaattatttaattgtattaggattaactctactcatttatcttttactgtatttttggtttgagactctggccaactgtt--------cctgttcacaattctcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
||||| | || | | | | || | | | | | ||| | | | || || | || | || | | ||||| |||||||||||| || ||||| |||||||| || |||||| |||| ||||| || || |||||||||||| | | |||||||| | ||| |||| ||||||
----attatctctttcttctt---tcacctatgtttggtgttggtataccatgctcaagcttgagaaccataatgaatttttgagatgattttctctgtaattc-cagGTTTATTGAAACATTTGGCACCCATATTATAGTTGGTGTGAAGATGGGCGGGAAGGATGTAATATATGTTAGACAGCAGCATGCTTCACCTCTTCAACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactgtatttttggtttgagactctggccaactgttcctgttcacaattctcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
ttctc CT-rich tract
tattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaattatttaattgtattaggattaactctactcatttatcttttactgtatttttggtttgagactctggccaactgttcctgttcacaattctcagGTTTATTGATACCTTTGGTACCCATATAATTGTTGGTATGAAAATGGGTGGAAAAGATGTAATATATTTGAAGCAGCAGCACTCATCAACTCTCCAACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - ctactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttcc