Sequence
atgc intronic sequence ATGC exonic sequencegtgatgctttaatacaattatatcacaatttcatcacagactttgagacgaaaatcaaccttctcaagcttgcacattttgctgttatagTTTCTCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTTATCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT
Basic information
species | Glycine max |
transcript | GLYMA09G34310.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 1
----------gtgatgctttaatac-----aattatatcacaatttcatcacagactttgagacgaaaatcaaccttctcaagcttgcacattttgctgttatagTTTCTCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTTATCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT
|| || || || | | | | || | | | || | ||| | || |||| | || | | | | || | | | || | | | || ||| | ||| |||| ||| | | ||| |
aaatttactcttgttgtttgaaccttgcttaggtttgtaactgctgtgttgtgccttctgcgtttttg--caattctaacagcggcatccattctcctacagACGGGTGACACCCTCATACAGCTCTACAACAATTTCATCACTGATTTCGAGACGAAGATCAATCTTCTCAA---ACTTGCGCATTTCGCGGTCATCGCTTCGC
upper sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
----gtgatgctttaatac--aattatatca-caatttcat-cacagactttgagacgaaaatcaaccttctcaagcttgca-cattt-tgctgttatagTTTCTCGGCAGTATTCTGAAAA---AGAAGCTGCTGTTGGTTATCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT
||| || ||| |||| ||| ||| || | || ||| | || ||| | | | || | |||| | || | || | || || || | | | || | | | ||| ||| | ||| |||| ||| | | ||| | |
tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAA---ACTTGCCCACTTCGCGGTCATCGCTTCAC
upper sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 2
gtgatgctttaatacaattatatcacaatttcatcacagactttgagacgaaaatcaaccttctcaagcttgcacattttgctgttatagTTTCTCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTTA--TCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT-------------------
| | | || | | | | | || | || | | | | ||| |||| || || | || | | | | | || || | | | ||| | | ||| | || |||| | ||| || | || ||
-------taaagtttgccaattttata---ttgttccaagtcatttcacctgctgctatttctgtactcttttgtcttttatgattctaatatcaccttttcttctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATCACTGATTTTGAGAC-CAAGATTAATCTGCTCAAGCTTGCCCATTTTGCGGTGATAGCTTCTC
upper sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
gtgatgctttaa----tacaattatatcacaatttcatcacagactttgagacgaaaatcaacct-tctcaagcttgcacattttgctgttatagTTTC---TCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTT-ATCTTGGAG---GGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT
| | | |||| || | | || ||| | || || |||| | | | | ||||| | ||| || | | | || | |||| || | | ||| || || || ||| || | | | | || | || || | | || | | |
-ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcatttcagGCTGGTGATGCTTTGATTCAGTT-CTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC
upper sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G19006.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------gtgatgctttaatacaattatatcacaatttcatcacagactttga-gacgaaaatcaaccttctcaagcttgcacattttgctg-ttatagTTTCTCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTTATCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT
| ||| | || || | |||| | || | || | |||| || ||| | | | | | ||||| | | || | || | | | || | || | | || ||| || | | | | || | | ||
cgaatattttagctcagagatacccaaaaact-cagctttacaaggtttacagatttgttaatgacgtgtttccccctgtttatgttcataatctttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAGACGAGGATCAATC-----TTCTGAAGCTTGCGCATTTCGCTGTTGTAGTCTCCC--
upper sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
-------------gtgatgctttaatacaattatatcacaatttcatcacagactttgagacgaaaatcaaccttctcaagcttgcacattttgctgttatagTTTCTCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTTATCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT
|| | | | || |||| || | | || | |||| | | || | ||| | || || | | | |||| | | | | | | | ||| ||| ||| ||||| | | | | || |||
ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTG--TCATAGTTTCTA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagactttgagacgaaaatcaaccttctcaagcttgcacattttgctgttatagTTTCTCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTTATCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT
ttttgct CT-rich tract
aaaatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatgctttaatacaattatatcacaatttcatcacagactttgagacgaaaatcaaccttctcaagcttgcacattttgctgttatagTTTCTCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTTATCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC