Sequence
atgc intronic sequence ATGC exonic sequencegtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
Basic information
species | Glycine max |
transcript | GLYMA08G22140.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
|| | | ||||| | | | || | || | |||| ||||| | | || | |||| || || || | || | |||| ||| | |||| |||||| || ||||| || ||||| || || |||| |||| |||||| || |||||||||||||||||||| |||||||| || |||
gtttgcgattttgttccttacatt-----tgcttggcatagtttttgc--atttctaacatttcttggtctggatttgaatgtggtgcccttat-------ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 7
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgc-agATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
||||| ||| |||| | | | | || || ||| | ||||| ||| || || || | || ||| | | ||| | |||| | ||||||||| |||||| || ||||| || ||||| || ||||||| ||| |||||| || ||||||||||||||||| || ||||||||| || || |
gtatacccatatgttttattttgttttaatgataatgtattaatttctcgttttcc-----tctttgctagcc-ttaacgagcaattttct----ttacttgaaatttctagATTTGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTGGATGGTCATTCAAAAGGTGTCAATTGTGTTGATTACTTCACTGGTGGTGACCGGCCATATC
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
----gtat-atacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatga-----taaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
|| | || | || || |||| | | | || | || ||| | || | | | | | || | || || | || | || ||||| ||||| |||| |||||| ||||||||||| ||||| || | |||| |||| ||||| ||||| |||||||||||||| || |||||||| ||| ||||
gtttgtgttatctccgctttaaaaattctggttg-gccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttt--tgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
|| || | || |||| || || | || | | || ||| | | | | || |||| | ||||||||||||||||| || || ||||| |||||||| |||||||||||||| |||||||| |||||||| ||||| || || |||||||| || || ||
------------gtgctga--aatggtctaacattgaaacatcattat--ggtttagtccgcttagtccgctcattctacgtttacatgc-------atgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 6
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
| | | | | || | || | | | || ||| | | | | | | | ||| || | || ||| | | |||| | ||||| ||||||||||| || || ||||| |||||||| ||||||| ||||| |||||||| || ||||| ||||| || ||||| ||||| ||||| || |
--gtgtgtaagaggtccaagcactgagcttttatgg-------cttagttagcacgaggtacttttaaaagggttttcttagactaattttcatgct-tgttcatattcagATATGGAATCTTGGTTCCCCAGACCCAAATTTTACACTGGATGCTCATCAGAAAGGAGTCAACTGTGTAGATTATTTCACAGGGGGTGATAAACCCTATC
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
||| | | || ||| || |||| | | |||| || |||||| || || || | ||||| | | | | | |||| ||||||||||||||||| || || |||||||| |||||||| |||| ||||| || || ||||| || |||||||| ||||| || ||||| ||||
gta-agattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacc-tagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
gtat-atacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
|||| || | |||| | || | |||| ||| ||||| ||| |||| | |||| | || | | | | | ||| | ||| ||||| | || ||||| ||||||||||||||||| ||||| |||||||| ||||||||||||| ||||| || ||||||||||||||||||||||| ||||| ||||| || |
gtatgatctggattttctgttggcaacttgttaactgcatttt-tttaccaattttgcttcatcaa--gtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatcta-tgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
| | ||| | | | ||| | ||| | | | || | | || | ||||||| ||| | || || | | | || |||||||||||||| ||||| |||||||| |||||||| ||||||| ||| ||||| || || |||||||||||||| || ||||||||||| || |||
-----------tatactt-taagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
tattaat putative branch site (score: 2)
ttatcttc CT-rich tract
tatgataaaaatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG