Sequence
atgc intronic sequence ATGC exonic sequencegtaattattttatttgattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
Basic information
species | Glycine max |
transcript | GLYMA03G05150.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 12
--------------------------------gtaattattttatttgattgttattcaaaa--------ccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
| | | | ||| || || |||| ||||| || || || |||||||| ||||| ||||| ||||||||| || | || ||| |||||||||||||||| ||||| ||||
gtaaaatattaaaatcttggtttgcaagatttttgaatgtcatataaatctgacataaaaaaaccatgtttcagGTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
upper sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
-------------------------------gtaattattttatttgattgttattcaaaac------cagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
| | | | || | || ||||| ||||| || || || ||||| || ||||| ||||| ||||||||| || | || ||| |||||||||||||||| ||||| ||||
gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
upper sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------------------------gtaatt--attttatttgattgtta--ttcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
||||| |||| || | | ||| | | | ||||| || || || |||||||| ||||||||| | ||||||||| | | ||||| || ||||| |||||||||||||| ||||
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
upper sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
---------------------------------------------------------gtaattattttatttgattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
|| || || | | ||||| ||||||||| || || ||||| || |||||||| |||||||||||| ||||||||||| | |||||||||||||||||||| ||||
gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatgagaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
upper sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 11
--------------------gtaattattttatttgattgt---tattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
| | | || || | || |||||||| || || |||||||| ||||| || || ||||||||| | | ||||| ||||||||||||||||||| || || |
gtgataggattgctcttgttcttgctttcctacacacgcgtacatgttgcgttgcagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG
upper sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 11
--------------------gtaattattttatttgattgt---tattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
| | | || || | || |||||||| || || |||||||| ||||| || || ||||||||| | | ||||| ||||||||||||||||||| || || |
gtgataggatttctcttgttcttgctttcctacacacgcgtacatgttgcgttgcagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaattattttatttgattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
atttgat putative branch site (score: 5)
taattattttatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattattttatttgattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA