Sequence
atgc intronic sequence ATGC exonic sequence...tatattgtaaatgttcattatgtattgtgattgaattgtacctcttgttcttctctgctggaataaaactatgtgagctaaagtatgtttaatttgacagGAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
Basic information
species | Glycine max |
transcript | GLYMA07G11310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g49600.2 (Oryza sativa), 3'ss of exon 2
-tatattgtaaatgttcattatgtattgtgattgaattgtacctcttgttcttctctgctggaataaaactatgtgagctaaagtatgtttaatttg--acagGAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
|| | |||| | | | | || || ||| | | || ||| | || | || ||| | ||||| | | | | || |||||||||| | |||||||| || ||||||||||||||||||||||| |||||||| |||||||| || || |||
aaatgctctaaaatatgcgtgtccaaggtc-ttacattacatgtaa-gtgtttccattctccattat--ctaaaaaa---aaagtgtatccattctggaacaggaagATGTTAATCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g49600.3 (Oryza sativa), 3'ss of exon 2
tatattgtaaatgttc---attatgtattgtgattgaattgtacctcttgttcttctctgctggaataaaactatgtgagctaaa-gtatgtttaatttg--acagGAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
|||||||| || | |||| | | | || | | ||| | | | | | ||| | | ||| || | | | | || |||||||||| | |||||||| || ||||||||||||||||||||||| |||||||| |||||||| || || |||
----ctgtaaatgctctaaaatatgcgtgtccaaggtcttacattacatgtaagtgtttcc--attctccattatctaaaaaaaaagtgtatccattctggaacagGAAGATGTTAATCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G118003_T02 (Zea mays), 3'ss of exon 2
tatattgtaaatgttcattatgtattgtgattgaattgtacctcttgttcttctctgctggaataaaactatgtgagctaaagtatgtttaatttgacagGAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
|| | |||| | | | || | | | | | | | | | ||| | | | | |||||||| | ||||||||| || ||||| |||||||||||||||||||||||||| |||||||| || || ||
---------gtacttaactatgcgaagcaaataaaccgatctgggctgagacacaagagagtttgatgcctttatcgttaactcttttgttctgcttcagGAAGACGTCGATCTCATGAAAAGTTTGAACTTTGATGCCTACCGGTTCTCAATCTCATGGTCCAGGATCTTCCCGG
upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 2
lower sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 2
tatattgtaaatgttcattatgtattgtgattgaattgtacctcttgttcttctctgctggaataaaactat----gtgagctaaagtatgtttaatttga----------------------------cagGAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
|| || | | ||||| | | | | | || | || | |||||| |||||| | || | ||||| |||| | ||| ||||||||| | || |||||| || ||||||||||||||||||||||| |||||||| |||||||| || || |||
-gtactgc---tccttattatatgacaatgctagagtccatctatctaggttttatgctggtgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 2
lower sequence: AC217401.3_FGT002 (Zea mays), 3'ss of exon 2
tatattgtaaatgttcattatgtattgtgattgaattgtacctcttgttcttctctgctggaataaaactatgtgagctaaagtatgtt-taatttg-acagGAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
| | | | | ||| || || | ||| | | | | | || || | | ||| | | || | ||| |||||||||| | ||||||||| ||| | ||||||||||| |||||||| |||||||| |||||||| || || |||
tgaaacgaacaaaa-catctcacgctgagaattaataattcatttagaaattagtaactatt-tcttttagtctgaatttggcttctttatcccttgtacagGAAGATGTTGATCTCATGAAAAGCCTAAATTTTGATGCATACCGGTTTTCAATCTCCTGGTCCAGGATCTTCCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcttctctgctggaataaaactatgtgagctaaagtatgtttaatttgacagGAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
taaagtatgtttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatattgtaaatgttcattatgtattgtgattgaattgtacctcttgttcttctctgctggaataaaactatgtgagctaaagtatgtttaatttgacagGAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA
- - - - - - - - - - - - - gtgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgtg