Sequence
atgc intronic sequence ATGC exonic sequencegtatgccaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttttttttcagaatgacacactcattccattcttctctttttccatatgtatgtgcatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGTTGTTATTCTTCTTCCATCAAATATTACTGTTTTTACTCTTGACTTCTCAGGGTCAGGCTTGTCTGATGGA
Basic information
species | Glycine max |
transcript | GLYMA15G12950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 3
gtatgccaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttttttttcagaatgacacactcattccattcttctctttttccatatgtatgtgcatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGTTGTTATTCTTCTTCCATCAAATATTACTGTTTTTACTCTTGACTTCTCAGGGTCAGGCTTGTCTGATGGA
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--------------------------------------------------gttatgagc-tagcatttcctcttaactgatgagattcatctca-agcaat-caccgatatc--ttttggaatctttaacaggcttttgctttgact-caatgcagTGGATGCCGGGCAGATGCAAATGAAGCTGCTGTTATACTGCTTCCTGCAAATATCACTGTTTTTACACTTGATTTTTCCGGGTCAGGTCTATCAGGTGGA
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 3
gtatgccaatttttatggatactgctatcactgcaagagattctatacggtttac-agtcataaagaccctttttgaacattcttttttttttcagaatgacacactcattccattcttctctttttccatatgtatgtgcatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGTTGTTATTCTTCTTCCATCAAATATTACTGTTTTTACTCTTGACTTCTCAGGGTCAGGCTTGTCTGATGGA
|| ||| || | ||| || ||| | | || || |||| || || | | | | || || || || | | || | |||||||||||| || || ||||| |||||||| | ||| || ||||| || |||||||| || | ||||| |||||||| |||||||||| | || | ||||
---------------------------------------gttagttacagtctctgagttattgagatgaatcattaattttgttttcttcttgtgcttatcgtattccttacaagctctttctcttaact------------------caatgcagTGGATGCAGAGCGGATGCAAATGAAGCAGCTGTCATACTTCTCCCTTCAAATATCACCCTCTTTACACTTGACTTTGCAGGGTCAGGGCTATCAGGTGGA
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 3
gtatgccaatttttatggatactgctatcactgcaagagattctatacggtttac-agtcataaagaccctttttgaacattcttttttttttcagaatgacacactcattccattcttctctttttccatatgtatgtgcatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGTTGTTATTCTTCTTCCATCAAATATTACTGTTTTTACTCTTGACTTCTCAGGGTCAGGCTTGTCTGATGGA
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-------------------------------------------------gcctatgagctatcaagatgattctt--atttccatttgctctttaccatcttcaat--atccaatgtggttcatttaacaagttttt---tat-taatttaatgcagTGGATGCAGAGCAGATGCAAATGAAGCCGCTGTCATACTTCTTCCTTCAAATATCACCCTTTTTACACTTGACTTTGCGGGATCAGGGCTATCAAGTGGA
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 3
gtatgccaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttttttttcagaatgacacactcattccattcttctctttttccatatgtatgtgcatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGTTGTTATTCTTCTTCCATCAAATATTACTGTTTTTACTCTTGACTTCTCAGGGTCAGGCTTGTCTGATGGA
||| || | | | | | | |||| | | || || ||||| | | | | ||| ||| | ||| | | || | ||||||||||||||||||||| ||||| || ||| | |||| || ||||| || || |||||||| || ||||||||||| ||||||||||| ||||| ||
--------------------------------------------gtaca---tagatacttgcacatctcttttaggaactaagaacttgttt---atgac-tagttgaataaataagaacttaatccgtttgtttcggaatctta------ccagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAACATAACTGTTTTCACCCTTGACTTCTCGGGGTCAGGCTTATCTGAGGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acactcattccattcttctctttttccatatgtatgtgcatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGTTGTTATTCTTCTTCCATCAAATATTACTGTTTTTACTCTTGACTTCTCAGGGTCAGGCTTGTCTGATGGA
atatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgccaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttttttttcagaatgacacactcattccattcttctctttttccatatgtatgtgcatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGTTGTTATTCTTCTTCCATCAAATATTACTGTTTTTACTCTTGACTTCTCAGGGTCAGGCTTGTCTGATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA