Sequence
atgc intronic sequence ATGC exonic sequencegtatgcagaatgtttcagtatctactatatagattttatttaaaggattgcattaatagaaacttactcatgttggacctgttcccaatttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
Basic information
species | Glycine max |
transcript | GLYMA08G42170.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G017386_T03 (Zea mays), 3'ss of exon 5
gtatgcagaatgtttcagtatctactatatagattttatttaaaggattgcattaa----tagaaacttactcatgttggacctgttcccaatttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
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gtattattcttttttctaacccatacctgctcatttgctttgtgtctttacaatgacttatagagtttaactttcctcatccatttttcttgcttcagATATGTTGCACCTGAATATGCTAATACTGGAATGTTAAATGAAAAGAGTGACGTTTACAGTTTTGGCGTTCTCTTGTTAGAAACTGTGACAGGAAGGAAT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------------------------gtatgcagaatgtttcagtatctactatatagattttatttaaaggattgcatta---------atagaaacttactcatgttggacctgttccca--atttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
||| || | || | | | | | | ||||| ||| | | | || | ||| |||| | | |||||| |||||||| || |||||||| || || ||| ||||||||||||||||||| | ||||| ||||| || || || || ||| |||||||||| |||||
gtatgttgtttgcttgatattctttcatttttgtagtaccttgcttgactaactggaacatgtggtattacagtaggaacctttacatgttgagggatttgtttttcatgtttttagagcagtataaagttttgtggtgcttcacatgacatgaaaagaaccattcaccttttgttgctactgtttcagGTATGTGGCCCCTGAATATGCCAACACTGGTCTGTTAAATGAGAGGAGTGATGTCTACAGTTTTGGAGTGCTACTACTGGAATCAGTTACTGGGAGGGAC
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------------gtatgcagaatgtttcagtatctactatatagattttatttaaaggattgcattaatagaa-----acttactcatgttgg-acctgttcccaatttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
||| | || | | | || | | | ||| | ||| ||| | || | | |||| || | | | | |||||| |||||||| || || ||||| ||||||||| |||||||||||| ||| || | ||||| ||||| || || || || |||||||| ||||| ||||||
gtatgtttttttatgggaacattccgaaatatgtcttttcttcactaactggaacctgtagtcttcacacgcagtaggaagtttacatacagagctttgttttccaatttttaagaagaattagctctgcaggggaagcaaccattcatctttttatttcaccacggtttcagGTATGTGGCTCCCGAGTATGCCAATACAGGTCTGTTAAATGAGAAGAGCGATGTCTACAGTTTTGGGGTGCTACTACTGGAAGCAGTGACTGGGAGGGAT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcagaatgtttcagtatctactatatagattttatttaaaggattgcattaatagaaacttactcatgttggacctgttccca-atttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
| ||| | | | | || | | | | ||| | || | | || || | | || | ||| | |||| ||||| ||||| |||||||||||||||||| | || ||||||| ||||||||| || ||||||||||| || ||||| || | | |||||||| |||
-------------gtaagtctaaaatttgtaccctctttggtgatgat-gggtttttgtatacatattattaacggtcatgtgtatatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 4
---gtatgcagaatgtttcagtatct----actatatagatt-ttatt-------taaaggattgcattaatagaaacttactcatgttggacctgttcccaatttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
| || || || | || | || || || ||||| | | ||| | ||| | || | | | |||||| |||| |||||| ||||| ||||| |||||||||||||||||| | ||||| || | |||||| || || ||||||||||| | || |||||||| | ||||| | |||
gtaaagtccaaaactttgtaccctcctcaggccattaaggttattattatcttctcagatgatgtccttacaaagaaatcattgatgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
----------------gtatgcagaatgtttcagtatctactatatagat-tttatttaaaggattgcattaatagaaacttactcatgttggacctgttccc--aatttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
| | || || ||| | || | | | | | | | || || | | | | | | || ||| | ||||||||||||||||||| |||||||||||||| || ||||||||||||| |||||| || ||||||||||||||||||||||| |||||||||||||||||||||
gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaggattgcattaatagaaacttactcatgttggacctgttcccaatttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
aacttac putative branch site (score: 2)
cctgttccc putative PPT
attaatagaaactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcagaatgtttcagtatctactatatagattttatttaaaggattgcattaatagaaacttactcatgttggacctgttcccaatttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG