Sequence
atgc intronic sequence ATGC exonic sequence...taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattgttattgctaactttgttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
Basic information
species | Glycine max |
transcript | GLYMA06G35660.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G393433_T02 (Zea mays), 3'ss of exon 1
taataactttctcttcgtaagataatcattgtg-gtggagaattatgccagaacattgttattgctaactttgttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
| || || | | || | || | | | || | ||| | || || || | | | | || || |||| || || |||||||| |||||||| ||||||||||| ||||| || ||||| |||||||| || || | |||||||| | ||||| | || || ||
------------gtgagtgagctgctttgcttgcatcgaccacccaccgattgaatagacattaagcttgtcgtgatgtgatgtgatctgatctg-atcagACAAGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTACAGCCTCCGCGACCGCAAGTACCCGACGGGCCTGCGCACCAACCGCGCCACGGTGGCCGGCTA
upper sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G139700_T01 (Zea mays), 3'ss of exon 1
taataactttctcttcgtaagataatcat-tgtg-gtggagaattatgccag-aacattgttattgctaactttgttatt-tgctattgtt--tcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
| | || || | | | | || | | | || | | || | | || ||| || | || | | || ||||| || || |||||||| |||||||| ||||||||||| |||| || ||||| |||||||| || || | |||||||| | ||||| | || || ||
--------gtgagtgagtgagtgggttacatatacgtacatactctcgctggtgatgaccgtaccgatcacccgactatgatgatgatgatgatgatgatgagcagACAAGGCGAAGATGGGGGAGAAGGAGTGGTACTTCTACTGCCTCCGCGACCGCAAGTACCCGACGGGCCTGCGCACCAACCGCGCCACGGCGGCCGGCTA
upper sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattgttattgctaactttgttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
|||||| ||| | | | | || |||| ||| | || || | || | | || | || || ||| |||||||| ||||| ||||||||||||| |||||| |||||||| ||||| || || ||| | | || || || || || || ||||||||
----------------gtaagaaaat-acaaaactaacttact-tgtagttcttttgtaattaaggtttctgaaatct-ttact-ctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
upper sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattgttattgctaactttgttatttgc-tattgtttcatatgtgg-cagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
|| ||| | | | | | | || | |||| | | | |||| | | || ||| | || |||| |||||||||||||| |||||||| |||||||||| ||||| || || || ||||| |||||||| | || ||||| ||||||| |||||||| ||
------------gttggtaccacctacctacccttctacattttctctcaaacacccacacaatccattaatttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
upper sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S279_85V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------taataactttctc-ttcgtaagataatcattgtggtggagaatt--atgccagaacattgttat-tgctaactttgttatttgcta-------ttgtttcat-------atgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
||| || | | | ||||| || | || | |||| || ||| | || | | | | ||||||| || | | | || | ||||| || || ||| | || ||||||||||||||||||| || || ||||||||||| |||||||| || || || || || ||||| || || ||
gtatttttttcttttcgcattatccttcagaacatttggtgtagacctaacaattgtgttattcgtgtagtaggaaacctgatacgaaatttagtgtaagattcgcatgatctacagaatgctttatttgtgggataaagctgctccgtctcgatgattttgcagATAAGGCCAAGGTTGGAGAGAAGGAATGGTACTTCTTCAGTCTGCGTGACCGAAAATACCCAACCGGCCAGCGAACTAACAGAGCCACTGATAAGGGATA
upper sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S159_57V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattg---ttattgct-----aacttt---gttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
| || | || | ||| | | || || || ||| |||| | | ||| || ||| || || ||| | | || | | | ||| |||||||| | | || |||||||| |||||||| | |||||| || ||||||||||| ||||| |||||| | ||||| || ||||| || || ||
gtatgcattgtttatttaaattaaattcaactttttaggatgctgcaccatggatttcattaggagtacaggatactgcggcaacactagattaattccttgaaaaacctttacagtacttgattcttgtttgttt-tctcagTGAAAGCAACGTTTGGGGAGAAGGAGTGGTACTTTTTTAGCCTACGAGACCGAAAGTATCCAACGGGATTAAGAACCAACAGAGCCACTGAGAAGGGCTA
upper sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ22540 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------------------------------------------------------------------taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattgttattgctaac-tttgttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
| || | ||| |||| | ||| |||| | || || | || | | | |||| | || |||| | ||||||||||||||| ||||| ||||||||||||||||||| |||| | | ||||| |||||||| || || | || || ||| |||| ||||| || || ||
gtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGGAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA
upper sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ11746 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------------------------------------------------------------------taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattgttattgctaac-tttgttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
| || | ||| |||| | ||| |||| | || || | || | | | |||| | || |||| | ||||||||||||||| ||||| ||||||||||||||||||| |||| | | ||||| |||||||| || || | || || ||| |||| ||||| || || ||
gtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGTAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA
upper sequence: GLYMA06G35660.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32111 (Selaginella moellendorffii), 3'ss of exon 1
--taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattgttattgctaac---tttgttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
|| | | || ||| | | || | | || | || | | | | ||||| || ||| || ||| ||| | || | |||| || || |||||||||||||||||||||||||||| | || || ||||||||||| || || ||| | ||||| || | |||||||| || || ||
ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgctccaca-----cagACAAGGCCAAGATGGGTGAGAAGGAATGGTACTTCTTCACGCTGCGGGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccagaacattgttattgctaactttgttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
tgctaac putative branch site (score: 1)
taactttgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taataactttctcttcgtaagataatcattgtggtggagaattatgccagaacattgttattgctaactttgttatttgctattgtttcatatgtggcagAGAAAGCAAAGATGGGTGAGAAGGAATGGTACTTCTATAGCCTTCGTGACCGAAAGTACCCAACTGGATTACGCACCAATAGGGCCACCGAAGCTGGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - -tggtgga
- - - - - - - - - - - - - - - - - - - - - tatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctattg