Sequence
atgc intronic sequence ATGC exonic sequence...ttattagtatgaaacccaagttttggtttagcttaatctgcatatatttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTGTTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
Basic information
species | Glycine max |
transcript | GLYMA05G00210.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------ttattagtatgaaacccaagttttggtttagcttaatct-----gcatatatttt--tggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTG--TTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
|| | ||| | | ||| | ||| || | | ||| ||| | | | | |||||||| |||||||| ||||||||||| || ||||| || ||||||||||| ||||| || ||| | |||||| || || || || | ||||| || ||
taagcatcgtgatggcgttatgagaagttaaattatgttttaagtcttataccagaaatttctctttattgattcttaacaagataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA----------------------------------------------
upper sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
---------------------------------------ttattagtatgaaacccaagttttggtttag---cttaatctgcatata--tttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTG--TTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
| || || || || ||| ||| | ||||| ||| | | || |||||||| |||||||| ||||||||||| || ||||| || ||||||||||| || | ||| ||| | ||||||||| || ||||| | ||||| || ||
atcatagtggctccatatagaagttaaatttgtcaaaatcttataccataaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA----------------------------------------------
upper sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------ttattagtatgaaaccca-agttttggtttagcttaatctgcatatatttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTG--TTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
|| || | | | || || ||||| ||| || | |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | ||| ||| | ||||||||| || ||||| | ||||| || ||
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA----------------------------------------------
upper sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
-----------------------------------------ttattagtatgaaaccca-agttttggtttagcttaatctgcatatatttt--tggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTGTTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
|| || | | | || | ||||| | || ||| |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | ||| |||| |||||
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT--------------------------------------------------------------------------
upper sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------ttattagtatgaaaccca-agttttggtttagcttaatctgcatatattt--ttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTGTTTCTC--TCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
|| || | | | || | ||||| | || || | |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | ||| |||| |||| ||||| || ||||| | ||||| || ||
ctaatcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA----------------------------------------------
upper sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G009154_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------ttattagtatgaaaccca-agttttggtttagcttaatctgcatatatttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTG--TTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
|| || | | | || ||| |||| ||| || | |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| | | ||| ||| | ||||||||| || ||||| | ||||| || ||
ttctaatcacagatagtcttaggaaaatttccatacaagttgcagttttgtctatattttatagcattgagagttcttatcagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCTGTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA----------------------------------------------
upper sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------ttattagtatgaaacccaagtttt-----ggtttagct----taatctgcatatatttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTGTTTC--TCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
|| ||| |||| | ||| || | |||| || |||||| | | | | |||||||||| ||||||||||| ||||| ||||| |||||||||||||||||||| || || || |||| || | ||||| |||||||| || || ||||||
aggatggcaagacacattgacaatggataatttgtgttcttaatatgcatttaaagagttctcaagatttaactaatctaatcttcctgt-cctatggcagTGACTTGGAATGTTACTTGCACGTATTCACAATTCCTGGCTCAGAAGACGCCTACATGTTGTGTCTCATTGTCATCGTTCTATAATAACACTATAGTATC----------------------------------------------
upper sequence: GLYMA05G00210.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------ttattagtatgaa-----acccaagttttggtttagcttaatct-gcatatatttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTGTTTC--TCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
||| | | ||| ||||| | | || ||| || | | | | || ||||||| ||||||||||| ||||| ||||| ||||||||| ||||||| ||||| |||||| |||| || ||||||| ||||| || | ||||| |||
agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC---------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTGTTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
ttcct CT-rich tract
aatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattagtatgaaacccaagttttggtttagcttaatctgcatatatttttggcagtgacctggaatgttacctgcacatattctcaattcctggctcagAAGACCCCAACTTGCCGTGTTTCTCTCATCCTTCTATAACAATACAATAGTAAACTGCCCTACCTGCACCTGTGGTTGCCAAAACAAAACAGAACCTGGC
- - - - - - aacccaa
- - - - - - - - - - - - - - - - - -atctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctgca