Sequence
atgc intronic sequence ATGC exonic sequencegtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgttcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
Basic information
species | Glycine max |
transcript | GLYMA04G37050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgt-tcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
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--------------------------------------------------gttactctccatctcatcatattgcaaacatattatcatactcacacagttgga-------atctcac-agtgctttactcttaa--attactttttccttctt-------agGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 5
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgttcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
| | | | | | | | || | ||| | | ||| | |||||| || | | | || |||||||||||| ||||| || |||||||| || ||||||||||| |||||||| || || ||||||||||| ||||| ||||||||||||||||| | || |
----------------------------------------------------------------------------gtacactctcccaatattgtcatgagttctggtgattcctcaa--gttagttgctgaatactctatgtataaatcctttttctcagGATGTTGTCACAGAGAATGAGTTTGAGAAAAGGCTTTTGGCAGATGTTATACCTCCAAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgttcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
||| || | | | | || || | | | || |||| |||||| |||| | | | || ||| | || | ||||||||||| ||||| || || ||||| || |||||||||| |||||||| ||||||||||||||||| ||||| ||||||||||||||||| | || |
------------------------------------------------------------gtacaatcccctacatatt-gccgtgctttt--tggtgattcctcgagttatttactgaacactctacttacaa--gtcctttttct------------cagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 20
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgttcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
| | ||| || || | || ||| | ||| | ||| || | | | | ||| ||| ||||||| ||| ||| || || | | ||| || |||| | | ||||||| ||| || ||||| |||||||||||||||||| | || |||||||| || || |||| || |||||||| ||||| || ||||||||| | ||||
-----------------gtagtcattttcttttgttatattaggactcgaacccgttaat--ccagctcagtctct--atgttgatcttc----agagttttggaaattgttttactgtatagagcttactgt----tctctctaacaat-------gtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
upper sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgttcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
|| ||| | | | || |||| | || | || | | ||| | | | || ||| | ||||||||||||||||||||| || ||||| || |||||| | ||||||||||||||||| ||||||||| || || |||||||||||||| || || ||||
--------------------------------------------------------------------------------gtaatttttgtaccttcatgcaactaatttttatctttaacaagttatattgattaaaatcaattta--tttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
tccctcttatgttttt CT-rich tract
ttatgttttttgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgttcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT