Sequence
atgc intronic sequence ATGC exonic sequence...tcagtcagcttattcatatcaattgtgatggtcagtctattagagtgaataatcaatttcaatgtccatgatttcttatttgaactactcaattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCGCAACAGACCAAGTCCTCTAGGGTTGCTATACCAG
Basic information
species | Glycine max |
transcript | GLYMA13G32940.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G129155_T01 (Zea mays), 3'ss of exon 12
----tcagtcagcttattcatatcaattgtgatggtcagtctattagagtgaataatcaatttcaatgtccatgatttcttatttg-aactac-tcaattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCGCAACAGACCAAGTCCTCTAGGGTTGCTATACCAG
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accggctataagtttatttg-gtcatctgt-ataatt-gtttgcttgcat---tgacctttcttgttttccttattcattcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G180335_T03 (Zea mays), 3'ss of exon 4
----tcagtcagcttattcatatcaattgtgatggtcagtctattagagtgaataatcaatttcaatgtccatgatttcttatttg-aactac-tcaattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCGCAACAGACCAAGTCCTCTAGGGTTGCTATACCAG
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aaatcgactaagtttattta-gtcatttgt-atgatt-gtttgctcgcat---tgacctttcttgttttccgtattcattcactagcaacaatattaattgtgcagGAAGATTACATAAACACATCGCACCCAAGTTTTATTGGTGGCAGCAAGGCTGTTGAGGAAGCACAGCAGCAAGTTAGGTCTGCCAAAACGTCTGCAGTGG
upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------------------------------------------------------------------tcagtcagcttattca--tatcaattgtgatggtcagtctattagagtgaataatcaatttcaa---------tgtccatgatttcttatttgaactactcaattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCGCAACAGACCAAGTCCTCTAGGGTTGCTATACCAG
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gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatt-tcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 13
-----tcagtcagcttattcatatcaattgtgatggtcagtctattagagtgaataatcaatttcaatgtccatgatttcttatttgaactactcaattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCGCAACAGACCAAGTCCTCTAGGGTTGCTATACCAG
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caaaccaaaaaaagaaaaaaaaagtagcaattgtatgcacttcatcaaagt---taagtgttttct-tgacaatggtctca-gtctaagcaattctattctgtagATGGACTACATAAATACTTCACACCCAAATTTTATTGGTGGAAGTAAAGCTGTGGAGATGGCATTGCAACAGATTAAGTCCTCTAGGCTGCCTGTACCTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|193340691|gb|FK307108.1|FK307108EST: GAGAACATGATTGCGCACCTCATAGAAATGGAG ATGGACTACATAAACACTTCCCACCCAAATTT-ATTGGTGGAAGCAAGGCA
genomic: GAGAACATGATTGCGCACCTCATAGAAATGGAGgtattgcact ... aattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCA
EST:
gi|254339195|gb|GR847912.1|GR847912EST: AAGGCCTTGAACCCTCAGAGAACATGATTGCGCACCTCATAGAAATGGAG ATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCA
genomic: AAGGCCTTGAACCCTCAGAGAACATGATTGCGCACCTCATAGAAATGGAGgtattgcact ... aattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaataatcaatttcaatgtccatgatttcttatttgaactactcaattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCGCAACAGACCAAGTCCTCTAGGGTTGCTATACCAG
atgatttcttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagtcagcttattcatatcaattgtgatggtcagtctattagagtgaataatcaatttcaatgtccatgatttcttatttgaactactcaattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCGCAACAGACCAAGTCCTCTAGGGTTGCTATACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - catatca
- - - - - - - - - - - - gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtc