Sequence
atgc intronic sequence ATGC exonic sequencegtaactctacattcaattctgttaatggagttttctctcaatcaactagtttagttatttgaaaattctgactaactgtaagttctcagTGAGCTGCCAGAATTTCTTGGTGGCAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
Basic information
species | Glycine max |
transcript | GLYMA04G03230.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G174990_T02 (Zea mays), 3'ss of exon 8
gtaactctacattcaattctgttaatggagttttctctcaatcaactagtttagttatttgaaaattctgactaactgtaagttctcagTGAGCTGCCAGAATTTCTTGGTGGCAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
| ||| || | | | ||| | | | | || || || | || ||||| ||| || | | |||||| |||||||||||||||||||||| |||| |||| | || ||||| || ||||| ||||| || ||| | || || ||||| |||||
----gttagtattttttttgtgtgccgtacatttatgttgttta-ttacttccattct----aatttctgcttaa-tgcatgcatgcagTGAACTGCCAGAATTTCTTGGTGGCAAATGCAATTGTATTGAA------GGTTGCCAAAGATCTGACAAAGGTCCTTGGAAGGATCCCAACATAATAAAG
upper sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------gtaactctacattcaattctgttaatggagt--tttctctcaatcaactagtttagttatttgaaaattctgactaactgt-------aagttctcagTGAGCTGCCAGAATTTCTTGGTGGCAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
| | |||| | | | ||| | || | | ||| | | || ||| | || ||||| | | || |||| |||||||||| ||||||||||||| |||||| |||| ||||| ||||||||||||||| ||||||||||| || ||| | ||||| | || ||||||
gttgagacatctcaatcctcttgtttggttcacatg-agtccaaaatatgatatagcttgtttggttcacatgagtccaaaatatgatatagcttcctaaccatttttggaactttttcagCCAGCTGCCAGATTTTCTTGGTGGCACTTGCACCTGTGCAGATCGAGGTGGTTGTATGAGATCTGATAAAGGCCCCTGGAATGACCCTGAGATATTAAAG
upper sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaactctacattcaattctgttaatggagttttctctcaatcaactagtttagttatt-tgaaaattctgactaa--ctgtaagtt-ctcagTGAGCTGCCAGAATTTCTTGGTGGCAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
| || | || | | || |||| | |||| | ||| | |||| |||||||| || || || |||| |||||||||| ||| | ||||| | ||||||||||| |||||| || ||||||||||| |||||||||||||| ||| ||||| | | || |||||
---gtatgagttttgagtccttaactgttttttttttcttatcatatctccagaatataattaaaactctgactatatttggaacttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGGTTGTATGAGATCTGATAAAGGGCCCTGGAAAGACTCTGAGATACTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctcaatcaactagtttagttatttgaaaattctgactaactgtaagttctcagTGAGCTGCCAGAATTTCTTGGTGGCAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
gactaac putative branch site (score: 1)
ttctc putative PPT
tagtttagttatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactctacattcaattctgttaatggagttttctctcaatcaactagtttagttatttgaaaattctgactaactgtaagttctcagTGAGCTGCCAGAATTTCTTGGTGGCAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA