Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttctttttttcagaatgacacactcattccattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA
Basic information
species | Glycine max |
transcript | GLYMA09G02050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 3
gtaagcaaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttctttttttcagaatgacacactcattccattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA
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--------------------------------------------------gttatgagc-tagcatttcctcttaactgatgagattcatctcaagcaat----caccgatatcttttggaatctttaacaggcttttgctttgact-caatgcagTGGATGCCGGGCAGATGCAAATGAAGCTGCTGTTATACTGCTTCCTGCAAATATCACTGTTTTTACACTTGATTTTTCCGGGTCAGGTCTATCAGGTGGA
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 3
gtaagcaaatttttatggatactgctatcactgcaagagattctatacggtttac-agtcataaagaccctttttgaacattcttttctttttttcagaatgacacactcattccattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA
|| ||| || | ||| || ||| | | || || ||||||| || | | | | | || || || || | | | | | |||||||||||| || || ||||| |||||||| ||||| || ||||| || |||||||| || ||||||| ||||||||| | |||||||| | || | ||||
---------------------------------------gttagttacagtctctgagttattgagatgaatcattaattttgttttcttcttgt--gcttatcgtattccttacaagctctttctcttaact----------------caatgcagTGGATGCAGAGCGGATGCAAATGAAGCAGCTGTCATACTTCTCCCTTCAAATATCACCCTCTTTACACTTGACTTTGCAGGGTCAGGGCTATCAGGTGGA
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G081642_T03 (Zea mays), 3'ss of exon 3
gtaagcaaatttttatggatactgctatcact-gcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttctttttttcagaa--tgacacactcattc---cattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA
||| || ||||||| || | || | | || | ||| ||| | || || ||| || | | || | | | ||||| | | ||| ||| | || | | || | | || | | | |||||| ||||| | |||||||| |||||||| |||||||| |||||||| |||||||| ||||| || || ||||||||||| |||||||| | || | ||
gtatttaa-cttttatgctccatgtttgcatttgtttgacgattcatagggtgcttctttatctcaacttttt---aagacttggttgtatgatccagaagctcaaacaatcactggtatgttttggaatattaaacaggattttgctttgactcaatgcagCGGATGCCGAGCAGATGCAAATGAAGCCGCTGTTATACTTCTTCCTTCAAATATCACTGTTTTCACACTTGACTTTTCTGGGTCAGGTCTATCCGGCGGG
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 3
gtaagcaaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttctttttttcagaatgacacactcattccattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA---------------------------
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----------------------------------------------------------------------------------------------------------------------------------------------ttgactcaatgcagcggatgccgagcagatgcaaatgaagccgctgttatacttcttccttcaaatatcactgttttcacacttgacttttctgggtcagGTCTATCCGGCGGGGATTATGTCAGTTTGGGTTGGCATGAG
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 3
gtaagcaaatttttatggatactgctatcactgcaagagattctatacggtttac-agtcataaagaccctttttgaacattcttttctttttttcagaatgacacactcattccattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA
| || || || |||| || || | | | ||| | ||| | | | | || | | || ||| | | || | | || || | |||||||||||| || |||||||| |||||||| ||||| || |||||||| |||||||| || | ||||| ||||||||| |||| ||||| | || ||||
-------------------------------------------------gcctatgagctatcaagatgattctt--atttccatttgctctttaccatcttcaatatccaatgtggt----tcatttaacaagttttt-tat-taatttaatgcagTGGATGCAGAGCAGATGCAAATGAAGCCGCTGTCATACTTCTTCCTTCAAATATCACCCTTTTTACACTTGACTTTGCGGGATCAGGGCTATCAAGTGGA
upper sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcaaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttctttttttcagaatgacacactcattccattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA
||| || | | | | | | |||| | | ||| ||| ||||| | | | || || || || ||| | | | ||||||||||||||||||||| ||||| || | | | |||| || ||||| || || ||||| || || |||||||| |||||||||||||| ||||| ||
--------------------------------------------gtaca---tagatacttgcacatctcttttaggaactaagaacttgttt-----atgactagttgaataaataagaa---cttaatccgtttgtttcggaatctta--ccagTGGATGTAGGGCAGATGCAAATGAGGCAGTTATGGTTCTCCTCCCATCTAACATAACTGTTTTCACCCTTGACTTCTCGGGGTCAGGCTTATCTGAGGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacactcattccattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA
ttttcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaaatttttatggatactgctatcactgcaagagattctatacggtttacagtcataaagaccctttttgaacattcttttctttttttcagaatgacacactcattccattcttctcttttcatatgtatgtacatgtacaatgatgcagTGGATGTAGGGCAGATGCCAATGAAGCTGCTGTTATTCTTCTTCCATCAAATATTACTGTCTTTACTCTTGACTTTTCGGGGTCAGGCTTGTCTGATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA