Sequence
atgc intronic sequence ATGC exonic sequencegtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
Basic information
species | Glycine max |
transcript | GLYMA13G43680.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gtaagtactttgattaggtgacatttagttatctgctcttttccttct---tatt-cattgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|| |||| ||| || || | | || | | | | || || |||| || | |||| || | || | || |||| |||| ||||| ||||| || ||||||||| |||| |||||||| || || || |||||||||||| |||||||||||
gtgagtaattttgttcctggatttaaatttttttttgcgtgtcatttggaatattatgatgctaaataggatctgctttcttat-ttgt---agAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gtaagtactttgattaggtgacatttagttatctgctcttttccttcttat-tcat--tgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|| |||| ||| || || | |||| | | | || || | || || | |||| || || | || |||| |||| ||||| ||||| || ||||||||| |||| |||||||| || || || |||||||||||| |||||||||||
gtgagtaattttgttcatggattcaaatttattttgcgtgtcatttggaatattatgatgctaaataggatccgctttcttat-ttgt---agAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
gtaagt--actttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaata--taattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|| ||| | | | || ||| ||||| || ||||| | ||||| | |||| || |||||| | | || | ||||||| || |||||||| || ||||| ||||| |||| || || ||||||||||||||||| |||||||||||
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaat-ttcatactgaaataactagttttgtcactgtattt---ttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
gtaa-gtactttgattaggtgacattt-agttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgt-cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|||| | | |||| | | |||| | | | | | | | ||| | | | | | | | | ||| |||| || ||||||||||||||||||||| ||||||||||||| || ||||| |||||||||||| |||| || |||
gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
gtaagtac-tttg--attaggtgacatttagtt----atctgctcttttccttcttat-------tcattg--tttaatat----aattttgt--tattaa--------tcttgtgt-cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|||| || |||| ||| | || | | || || | ||| | || ||| || | || | ||| | || ||| |||| | | | | | ||| |||| || ||||||||||||||||||||| ||||||||||||| || ||||| |||||||||||| |||| || |||
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 14
----gtaagtacttt-gattaggtgacatttagttatctgctcttttccttcttattcattgtttaatataattttgtt--attaatcttgtgtc------agAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|| |||||| | || | | || ||| | |||| |||| || |||| | | | |||| ||||||| | |||| | || |||||||||||||||||| | || ||||| || |||||| | |||||||||||| |||||||||||
gtgagtcgttacttttgcttcagcaatggatacccatcatgtgtttttactcttttttgcc--ttaacgccactggaattgattactcttgtgcctggtgtagAATGTATATTGGGCTGACAGTGGTGATTTGGTGACAATAGCAAGCGATTCGTCATTCTACATTTTGAAGTACAAT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgtc---agAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|| | | | | ||| || || ||| | ||| ||||||||| | | || || ||| ||||| |||| | ||||||||||| |||||||| ||||| |||| || || ||||||||||||||||| || |||||||||
----gtgagtcaaaagtattatttttccttgggtggaaattttgtatgtatga---gtttaatattaaccttttgtttatcatgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
gtaagtactttgattaggtgacatttagttatctgc-----tcttttccttcttattcatt-gtttaatataattttgttattaatcttgtgt---cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
| || | || |||| | | | | || | | || || ||||| ||| | | || || ||| || | ||||| | ||||||||||| |||||||| ||||| |||| || || ||||||||||||||||| || |||||||||
--------gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
--------------------------------------------------------------------------------------------gtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaa--tataattttgttattaatct--tgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
|| || ||| ||| ||||| | | | | || | || | | ||| || || || || ||| |||||| || || ||||| ||||||||||||||||| ||||||| || ||||||||||||||||| || |||| ||||
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------------------------------------gtaagtactttgattaggtgacatttagtt--atctgctcttttcctt-cttattcattgtttaat--ataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
| || | | | |||| || | || ||||||| || || || | |||| || | ||| || | | | || ||||| || || |||||||||||||||||| ||||| | |||||||| || |||||||||||||| |||| | |||
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttg-cagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------gtaagtacttt--gattaggtg---acatttagttatctgctcttttccttcttattcattgtttaatataattttgt-----tattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
| | | ||| ||| || |||||| || || | | || | | | ||| | ||| | | | || || | || ||||| || || |||||||| ||||||||| ||||| | |||||||| ||||| ||||||||||| |||||||||||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttg-cagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
--------------gtaagtactttgattag-gtgacatt-tagttat-ctgctcttttccttcttattcattgtttaatataattttgttattaatct---tgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
| | ||| || ||| ||| | | || | | || | ||| | |||| | | ||| | || | | | | |||||||||||| |||||||| ||||| ||| | || | ||||| || ||||||||||| ||||| ||||||||||||
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttttccttcttattcattgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
tattaat putative branch site (score: 2)
ttcttattcattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtactttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG