Sequence
atgc intronic sequence ATGC exonic sequence...agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
Basic information
| species | Glycine max |
| transcript | GLYMA06G15520.1 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g36650.1 (Oryza sativa), 3'ss of exon 1
agagtttgaag--taaaccctcaa---agtctgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAA---AATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| |||| || | || | | | | | | ||| || | || |||| | |||| || | | ||||||| | || | || || | || ||| ||||||||| || ||||| ||||| |||||||| |||||||||||||| |||||||| |||
tgtttttgtaggatgaatgtttagttcaagttacatttttctgtatta-atctatagtctttgtaaacactgttttg--aatgatttattttgtg--ttatgcagATCAGTTAAAATAAATGGCTGACGCAGAGGACATTCAGCCCCTTGTCTGTGACAATGGAACCGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 1
-agagtttgaagtaaaccct-caaagtctgtaaatggctgggttctgta--gattgtctattcaaacttggtggtactgacaattta-ttgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| | | | | || || ||| | || | || || | | || | ||| | || || || | | | | ||| | || |||||||||| | ||||||||| || || ||||| ||||||||||| ||||||||||| |||
agcacctcaagatttcctctgcacagtatagtaactatcgaaaaagatattatttctttgtttttaattgacaaccttcacgtgctacttatttttgcagAGTAAATCTATAGGAAATGGCTGACGGTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 3'ss of exon 1
agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| || | | || || | || | | | ||| | ||| | ||| | || || |||| | | | | || ||| |||||||||| | |||||| || || || ||||| ||||||||||| ||||||||||| |||
-atgatttagttgaa-----gaaatgcgtcg-tcgtcgagttgtatagcaacaatgatcaggcactactac-ttgttaaagtattaactctctgcagctcttctgtagGAAATGGCTGACGGTGAGGACATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g01600.1 (Oryza sativa), 3'ss of exon 1
agagtttga-agtaaacc--ctcaaagtctgtaa-atggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
|| | | | | | || || | | | ||| | ||| | ||| | || || |||| | | | | || ||| |||||||||| | |||||| || || || ||||| ||||||||||| ||||||||||| |||
agtactcatcaatgatttagttgaagaaatgcgtcgtcgtcgagttgtatagcaacaatgatcaggcactactac-ttgttaaagtattaactctctgcagCTCTTCTGTAGGAAATGGCTGACGGTGAGGACATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 1
agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagattgtctattca-aacttggtg------gtactgacaatttattgtatgcgtactgtagTT--------TGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
||| ||||| | || | || || | | | | | | || | | ||| || || || | | || | | ||||| | | | | | | |||||||||| | ||||| || || |||||||| ||||||||||||||||| ||||| |||
agattttgattt---cctggagggtttgcgtctagtttctgttggaaaatggccatttcgtgacgtgttgcggcgcatgcctgttgttctgtttttgcgtcagGAATTCAGAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g06390.5 (Oryza sativa), 3'ss of exon 1
---------agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTT-TGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
|| ||||| | || | ||||||| | || | | | || | || || | ||| ||| | | | | | | | | | |||||||||| | ||||| || || |||||||| ||||||||||||||||| ||||| |||
atttcctggagggtttgcgtctagtttct---gttggaaaatggccatttcgtgacgtgttgcggcgcatgcctgttgtt-ctgtt--tttgcgtcaggaattcagAACCAGTAGGAGGAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTGTGTGACAATGGAACTGGCATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 1
agagtttgaagtaaaccctcaa--agtctgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| | || ||| ||||| || | | | | | ||| | || | || | || |||| | | | | | || |||||| || | ||||||||| || || ||||| ||||||||||| ||||||||||| |||
-aatcatagttctggcctgcaactagtctagcaagaaatatggtaaaaatttattctgtaacaagtaaatgatggagatggcttatgatttccttgttcagATT--------AATGGCCGACGGTGAGGATATCCAGCCACTTGTATGTGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G126190_T03 (Zea mays), 3'ss of exon 1
--agagtttgaagtaaaccctcaaagt-ctgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
|| || || || | || | |||| || | | || ||| || | | ||| || | ||| || | | | | |||| |||||||||| | |||||| ||||| |||||||||||||||||||||||||| ||||| |||
gctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctgt-tacttatcctttgtctcctcgtgtttttgttcca---gcatcat----cagTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G126190_T02 (Zea mays), 3'ss of exon 1
--agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagat-tgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagT----TTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
|||| | ||| | | | || | |||| | || | || | ||||| || | | || | | || | | | || | |||| |||||||||| | |||||| ||||| |||||||||||||||||||||||||| ||||| |||
gtttcctttgctgaaaatgcagctaataccaaacttgctgtttcctattgagatagatattctg--ttacttatcctt-tgtctcctcgtgtttttgttccagCATCATCAGTAACAAATGGCTGACGGTGAGGACATTCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 1
---agagtttgaagtaaaccctcaaagtct-gtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgt-----atgcgtactgtagTTTGGTAAA---AAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| | | | | | | | |||| | || | ||| | |||| ||| || | | |||| || || || | |||| | || || | | || |||||||||| || ||||| ||||| ||||| || ||||||||||||||||||||||| |||
taggcacatcagccttttctcccttactgaagtaattagcacatatttgtctacagtcttggtaaa--tgcttctcctgataaattgttttcattcatgcagATTGCAGATCATTTAACATAAATGGCTGACGCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 1
---agagtttgaagtaaaccctcaaa--gtctgtaaatggctgggttctgtagattgtct-attcaaacttggtggtactgacaatttat-tgtatgcgtactgtagTTTGGTAAA---AAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| | | | |||| || || | | | | | || | |||| | | || ||| | | | || ||| | | |||| | || || | | || |||||||||| | ||||| ||||| ||||| || ||||||||||||||||||||||| |||
tgtcattccttgtgctattgcacaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 1
---------------agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagat--tgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| | ||| | | | || | | |||||| | | | || | | |||||| | || | || ||| | || | | | || || |||||||||| | ||||| || || |||||||||||||||||||||||||| ||||| |||
aatgcagttttcttgttaataccaagcattctgccgtttcctattgagatagatattctgttactgatttttaccctagcttggtc-tcctctcctcctagTGTTTTTGTTCCAGAATCTG-TAGCAAATGGCTGACGGCGAGGACATCCAGCCCCTTGTTTGTGACAATGGAACTGGCATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053299_T01 (Zea mays), 3'ss of exon 1
agagtttgaagtaaaccctcaaa--gtctgtaaatggctgggttctgtagattgtctattca-aacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| |||| ||| ||| | || |||| | ||||| || | || | | | || | | || || | | ||| | || | ||||||||| | ||||||||| || || ||||| ||||||||||| ||||||||||| |||
--------acttaaatttccaagccatctagcatgaactaggttaaaaaaattgtgctttaacaagtgaatatttgagatggtct-ctgaattcagattgtc-tgtgcagATCAATGGCTGACGGTGAGGATATCCAGCCACTTGTGTGTGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 1
agagtttgaagt-aaaccctcaaagtctgta-aatggctgggttctgtagattgtctattcaaacttggtggtac-tga--caatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| | | | ||| || | || | || | || | | || | ||| | | || ||| | || || | | | | |||| ||| ||| ||||||||| |||||| || || || ||||| || |||||||| ||||||||||| |||
-gcatgcacattcaaatccactgttccttttcaaccacatagtgaaccaaaaca-ctctcatcactgagcgatatatgattctatccatatgccacttgcagCAGTTCTGTAGAAA-TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110378_T03 (Zea mays), 3'ss of exon 2
agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtat-gcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| | | | | | | || | || || | ||| | || | | | | || | ||| |||| || ||| ||||||||| |||||| || || || ||||| || |||||||| ||||||||||| |||
-caaatccagtcttccttttcattcacatgttgaactaaaacactttcatcactggttggtatttgattctatccatatgccacattgccgcttgctgcagTTCTTTAGAAA-TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G110378_T01 (Zea mays), 3'ss of exon 1
agagtttgaagtaaaccctcaaagtc-tgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtat-gcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
|| || | | || | || | || || | ||| | || | | | | || | ||| |||| || ||| ||||||||| |||||| || || || ||||| || |||||||| ||||||||||| |||
----------gtcttccttttcattcacatgttgaactaaaacactttcatcactggttggtatttgattctatccatatgccacattgccgcttgctgcagttctttagAAA-TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G067985_T12 (Zea mays), 3'ss of exon 1
-agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagattgtctattcaaacttggtggtac-tga--caatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| || || | || | | | || | | | | ||| ||| || | | || ||| | || || | | | | |||| ||| ||| ||||||||| |||||| || || || ||||| || |||||||| ||||||||||| |||
tgcacattcaaatccactgttcc--ttttcaaccacatagtgaaccaaaacactctcatca--ctgagcgatatatgattctatccatatgccacttgcagcagTTCTGTAGAAA-TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
agagtttgaagtaaaccctcaaagtctgta-aatggctgggttctgtagattgtctattcaaacttggtggtac-tga--caatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
||| || | || | || | || | | || | ||| | | || ||| | || || | | | | |||| ||| ||| ||||||||| |||||| || || || ||||| || |||||||| ||||||||||| |||
-----------caaatccactgttccttttcaaccacatagtgaaccaaaaca-ctctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAA-TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G18780.1 (Arabidopsis thaliana), 3'ss of exon 1
-agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagatt--gtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG------------------------------
| | ||| | | | | || | | | | |||| || | ||| ||| ||| || |||| || || || | |||||||||||||| ||||| ||||||||||| | || ||||||||||| || || |||||||||
gaaactttaggatttgtagtgtcgtacgttgaacagaaagctatttctgattcaatcagggtttatttgactgtattgaactctttttgtgtgt---ttgcagCTCA-TAAAAAATGGCTGAGGCTGATGATATTCAACCAATCGTGTGTGACAATGGTACCGGTATGGTGAAGGCTGGATTTGCAGGAGATGATGCTCCCAGG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 1
agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagatt--gtctattcaaacttggtggtactga--caatttattgtatgcgt-actgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
||||| | || | | | | | || || |||| | | || | ||| || | | || || | || | | | | || || | | || | ||||| |||||||| || |||||||| |||| ||||||||||| ||||||||||| |||
----attgaattgaatctactca-tgaatgaaaagcctggtttgattaagcaagtgttttcggttttctcgatcaagattcagatctttatgtttttgattgcagATCG-TAGACCATGGCCGATGCTGATGACATTCAACCTATTGTCTGTGACAATGGTACTGGAATGGTTAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 1
agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgac-aatttattgtatgcgtactgtagTTT------GGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
| ||||| || | ||| || || ||| || | | | | |||| || | | |||| ||| | | || ||| || ||||||||| |||| |||||||||||| || ||||| |||||||||||||||||||||||||||
---------aataaacgctgctaatcttcgaa--actaagttgtg-atctgattcgtgtttacttcatgagcttatccaattcatttcggtttcattttactttttttttagTGAAAAATGGCCGATGGTGAGGATATTCAGCCACTTGTCTGTGACAATGGAACTGGAATGGTGAAG
upper sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 2
agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagattgtcta--ttcaaacttggtggtact--gacaatttattgtatgcgtac--tgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
|| | | | ||| || ||| || | ||| | | | | |||||| || |||| | | | | | || | || || | ||| ||||| ||| |||| ||||| || ||||| || |||||||||||||||||||||||||||
-----atggaaattatctgaaaaagcta-aaaaggtgaatatttgtcaagcagcaaaacttaaactttgttatactttgtcccctgacttcatatttctcatgcagGTAATAAAAGGATGGCCGATACTGAAGATATCCAGCCCCTCGTCTGTGACAATGGAACTGGAATGGTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagattgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
tactgac putative branch site (score: 1)
acaatttattgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agagtttgaagtaaaccctcaaagtctgtaaatggctgggttctgtagattgtctattcaaacttggtggtactgacaatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
