Sequence
atgc intronic sequence ATGC exonic sequence...gatgactggtccggttttcaaaaccttgtgttcaagttcagtatttttgagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG
Basic information
species | Glycine max |
transcript | GLYMA18G46420.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
gatgactggtccggttttcaaaaccttgtgttcaagttcagtatttttgagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG
|| ||||| | || | | | || | || ||| ||| || ||| | ||| | |||| || | || | | || ||||| ||| | || |||||| |||||||||||||||||||| || | || |||||||| ||||| |||||||||||||| || ||||||||||| || ||||
----gtatgtatatttttctta---ttatatcccagccttgcatagttgcattccttgaatctactttg-catgttgttttactctctcattt----cagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
upper sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 10
gatgactggtccggttttcaaaaccttgtgttcaagt-tcagtatttttgagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG
|| | || | | ||| | ||| || | | | | | | | ||| | | |||| || | | || | || | | |||||| || | || |||||| | ||||| |||||||||||| | |||| |||||||| || || |||||||||||||| || ||||| ||||| |||||||
--------gtttgtattctatatgcttattttctagcctttgcactgcttaaaagttaaaactacttttgattt--tatggtactactattc-----acagGCTGGGTTATCGATGGCACTTGGAGCTTTTTTGGCTGGTCTGTTACTAGCAGAAACAGAGTTCTCCTTACAGGTTGAGTCAGATATAGCTCCTTATCGTG
upper sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 18
lower sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 10
gatgactggtccggttttcaaaaccttgtgttcaagttcagtatttttgagttcattaaattgatcttgacttgtt----tttgtt-ttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG
|| | || | | ||||| | | ||||| | | | | | | ||| | ||| | || || |||| ||||| |||| ||||||||||||||||| ||||| |||||||||||| ||||||| ||||| |||||||||||||| || |||||||| ||||| |||||||| ||||
--------gtatg-ttcttgattttccgtgttggtgcttggtattctcgtaattttgctttgtcttttgtttcgttaagataaattgtttctttctttaaattagGCGGGACTTTCCATGGCATTAGGAGCGTTTTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTG
upper sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 11
gatgactggtccggttttcaaaaccttgtgttcaagttcagtatttttgagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG
| | ||||||| | || |||| ||| | | | || | || | || || ||| |||| ||||| ||||||||||||||||| ||||| |||||||||||| |||| || ||||| || |||||||| || || || ||||| |||||||||||||||||||
-----------gtatgaccgtgaccttgt--tggcattgagtagtttactgacatgccagtacttcccgtctgctaatttttccagtttctataaatcagGCTGGACTTTCCATGGCATTAGGAGCGTTTTTGGCTGGTCTACTCCTTGCAGAGACAGAATTTTCGTTGCAAGTAGAATCAGATATTGCTCCATATCGTG
upper sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 9
gatgactggtccggttttcaaaaccttgtgttcaagttcagtatttttgagttcattaaattgatcttgacttgtttttgttt-------tcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG
| | | | |||||| || | || ||| | || || || || ||| | ||| ||| | || ||| | |||||||||| ||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||||||||||||||| |||||||||||||||||||
---gtattggatgcttttcataat----tattattattc--ttttcttataccaatcaagttgtgtctcccttttttccttaagaaaaaatcatttttcttgaacagGCAGGCCTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTGCTTCTTGCAGAAACTGAATTTTCCTTACAGGTTGAATCAGATATTGCTCCATATCGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG
tcttgac putative branch site (score: 3)
cttgtttttgttttcc CT-rich tract
ttcattaaattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgactggtccggttttcaaaaccttgtgttcaagttcagtatttttgagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG
-atgactg
- - - - - - - - - caaaacc
- - - - - - - - - - - - - tgtgttc