Sequence
atgc intronic sequence ATGC exonic sequence...aatgcaatttttttaccagccttattgtttctccctttgttaatttttctgttgaattgttttcatgtatcaagaattaatacattcttcatctatgcagGTATTCGCGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
Basic information
species | Glycine max |
transcript | GLYMA09G40290.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g22640.1 (Oryza sativa), 3'ss of exon 4
aatgcaatttttttaccagccttattgtttctccctttgttaatttttctgttgaattgttttcatgtatcaagaatta-atacattcttcatctatgcagGTATTCGCGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
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cttagggatgccccactaagctatgttttgtttagcatcttgatcatgttaatgcaatactaa-ataactgagacatcacgttttgtcatgttgtgtaaagGTATTCGCATTCAAAATATTCAGCCAGGCCAAATCATAATGGATATAGATCTTCGTTGGGGTGGTGATCCAAGCATAATCCTTGCTGTTGATGCTGTTGT
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G092129_T02 (Zea mays), 3'ss of exon 4
aatgcaatttttttaccagccttattgtttctccctttgtt--aatttttctgttgaattgttttcatgtatcaagaattaatacattct------------tcatctatgcagGTATTCGCGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
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--------------cccttttttattgcatttatatctgcttgaatcttgatgcaggactacataagtgcttaaaaaaatgatgggttttgtttgtttgttgtgatttgcgaagGTATTCGTATTCAAAATCTTCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGT
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G61050.1 (Arabidopsis thaliana), 3'ss of exon 5
aatgc-aatttttttaccagccttattgtttctccctttgttaatttttctgttgaattgttttcatgtatcaagaattaatacattcttcatctatgcagGTATTCGCGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
|||| ||| | || | | | || ||| | || ||| || | | | | | | | || |||| |||||||||||| ||||| ||| | || |||||||| ||| ||||||| ||||| | || |||||||||||||| ||||||||||| | ||| |||||||||
-atgctaatgaatccttgtgcttgaaagaacatcatgcagttgtctcttaggttagttttgctgtaagcctgagcatatgcataataaatcattgttgcagGTATTCGTGTTCAAAGTTTCAAGGAAGGTCAAGTCACAATGGACGTTGATCTTCGATGGGGTGGTGATCCAAATATTGTTTTAGGTGTGACAGCACTTGT
upper sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0048g01410.t01 (Vitis vinifera), 3'ss of exon 5
aatgcaatttttttaccagcct-tattgtttctccctttgtta-atttttctgttgaattgttttcatgtatcaagaatta-atacattcttcatctatgcagGTATTCGCGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
||||| | | | | | ||| ||| ||| | | | | | |||| || | || || ||| | || ||| ||||||| ||||| ||||| || ||||| ||||| ||||| |||||||| || || || || |||||||||||||| | ||| |||| ||||||||||| | |
---ccaattcacatgtcgccatatgaaagttcagcctgccttataaatcacaatgcatttgtctttgagcatttgtgcttgcataattactgaatcaatgcagGAATTCGTGTTCAAAGCCTTAAGAAAGGGCAAATTATAATGGATATCGACTTGCGATGGGGTGGTGATCCAAGCATTATTTTAGCTGTTGAAGCTGCTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctgttgaattgttttcatgtatcaagaattaatacattcttcatctatgcagGTATTCGCGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
aattaat putative branch site (score: 3)
ttcttcatct putative PPT
tatcaagaattaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgcaatttttttaccagccttattgtttctccctttgttaatttttctgttgaattgttttcatgtatcaagaattaatacattcttcatctatgcagGTATTCGCGTTCAGAGTCTTAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
aatgcaa
- - - - - - - -ccagcct
- - - - - - - - - - - - - - ttctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacattc