Sequence
atgc intronic sequence ATGC exonic sequence...caggcattcatattgactttgtggtgaatttcaatgttcaaacataagcatattaattggttaaatcactaattgtgtatttgctctctccttctttcagGATGGAAAAATAGAAGCTGAGGTCAAGCTCACGGGAATTCTCAGTTTAGGAGCATTGCAACCAGGTGAAAGTCGAAAATATGGCACGACTATTGCACCTG
Basic information
| species | Glycine max |
| transcript | GLYMA02G04360.1 |
| intron # | 7 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 7
caggcattcatattgactttgtggtgaatttcaatgttcaaacataagcatattaattggttaaatcactaa---ttgtg--tatttgct--ctctccttctttcagGATGGAAAAATAGAAGCTGAGGTCAAGCTCACGGGAATTCTCAGTTTAGGAGCATTGCAACCAGGTGAAAGTCGAAAATATGGCACGACTATTGCACCTG
| || | | | | | || || || | | | || | || | || | || | || |||| |||||| | ||| | || |||||||| |||||||| || || || ||||| || ||||||||||||||||| || ||| || || ||| | ||||||||||| |||||||| ||||
---gaatggaattcaattctaagg---atccaaacggg-gactaagaggaaataattttctgaagcttcaaagttttgtaattatttgttgatcctcttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCTG
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 7
----caggcattcatattgactttgtggtgaatttcaa-tgttcaaacataagcatattaattggttaaatcactaattgtgtatttgctctctccttctttcagGATGGAAAAATAGAAGCTGAGGTCAAGCTCACGGGAATTCTCAGTTTAGGAGCATTGCAACCAGGTGAAAGTCGAAAATATGGCACGACTATTGCACCTG
|| | || |||| ||| | | | ||| | || | | || || || ||| | ||| || || | | || || | |||||||||||||| ||||||||||| || ||||| ||||||||||| |||||||| |||||||||| |||| ||||||||||| || |||||||||||||
aattttggtgct-attttgaatttttatttactttttcctttttctgttgaggtatgctactta---aaaacttcaataatgccttaattgtatc-ttgatacagGATGGAAAAATTGAAGCTGAGGTTAAACTCACAGGAATTCTCAGCTTAGGAGCCCTGCAACCAGGGGAAATCCGAAAATATGGTACAACTATTGCACCTG
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ19345 (Selaginella moellendorffii), 3'ss of exon 5
caggcattcatattgactttgtggtgaatttcaatgttcaaacataagcatattaattggttaaatcactaattgtgtatttgctctctccttctttcagGATGGAAAAATAGAAGCTGAGGTCAAGCTCACGGGAATTCTCAGTTTAGGAGCATTGCAACCAGGTGAAAGTCGAAAATATGGCACGACTATTGCACCTG
|| || | ||||| | | | | | || ||| | || | ||||||||||||||||| |||||||| ||||||||||| |||||||| | |||||| | | | || |||| | ||||| || || ||| || ||||
-------------------------------------------------gtaagaacttgttaatggagtgacggcttgtt-actccgtgctagta-cagGATGGAAAAATAGAGGCTGAGGTGAAGCTCACGGGGATTCTCAGCCTGGGAGCACTTCGTGCTGGAGAAATCAGGAAATACGGGACTGTTATAGCTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagcatattaattggttaaatcactaattgtgtatttgctctctccttctttcagGATGGAAAAATAGAAGCTGAGGTCAAGCTCACGGGAATTCTCAGTTTAGGAGCATTGCAACCAGGTGAAAGTCGAAAATATGGCACGACTATTGCACCTG
cactaat putative branch site (score: 2)
tgtatttgctctctcc putative PPT
tattaattggttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caggcattcatattgactttgtggtgaatttcaatgttcaaacataagcatattaattggttaaatcactaattgtgtatttgctctctccttctttcagGATGGAAAAATAGAAGCTGAGGTCAAGCTCACGGGAATTCTCAGTTTAGGAGCATTGCAACCAGGTGAAAGTCGAAAATATGGCACGACTATTGCACCTG
- -gcattca
- - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - -caatgtt
- - - - - - - - - - - - - - - - - - - caaacat
