Sequence
atgc intronic sequence ATGC exonic sequencegtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
Basic information
species | Glycine max |
transcript | GLYMA08G22140.1 |
intron # | 7 |
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 7
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
| ||||||| || | || ||| | | | | | | | | | | | | || || |||| ||||| ||||| || ||||| || || ||||| ||||| || ||||| || |||||||| | ||||||||||| || |||||||| || |||||||||||||
----------------gttttttttttctatcca-cttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgtggtcatgg------tgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 7
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
| | || | | || | | || |||||| | | ||| ||| | | | | ||||| ||||| |||||||||||||| || || ||||| || || || ||||| || |||| ||||| ||||||||||| || ||||| || |||||||||| |||
---------------------------------gtatgccatctgcagtgaattatcttgtgagtatat---tggacattgttacg--agacacttcgttgaatcagGTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCACATAATGTCTCTGCTGTTTGTTTCCATCCGGAGTTACCTATAATACTTA
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
| |||| || | ||| || ||| | | | ||| | | | | ||| || | ||| |||| ||||| || || || || || ||||| ||||| || ||||| || ||||| ||| | ||||||||||| || |||||||| || |||||||||||||
----------------gtacaattttgtactcagctgtatgttttgagtgtttgattgt---tctatccagtcctaaggtggtgtgctt-tatggc----aaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 6
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
| | || | | | || ||| | |||| | |||| |||| ||| | | ||||| ||| | |||| ||||| || || || ||||| ||||| ||||| || ||||| || ||||| || | ||||||||||| || |||||||| || |||||||||||||
-----------gtacatttttgtactgaggtgtatgttctgaattttttgttgctctatgca-gtattatgatggtgcgttttatggcaa------------agtagGTCTGGGATTACCAGACGAAAAGCTGTGTTCAGACACTTGAAGGGCATACACATAACATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
gtttgttttctat-tttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
||| ||||| || | |||| |||| ||| || || | ||||| || | || || | | | | || ||| |||||||||||||||||||||||||||||||||||||| ||||| || |||||||||||||| ||||| || || || ||||| || || || ||||| || |
---------gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaat-tatgtatttgca----gatcgtt-tactagtggtactttt---tcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------------gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattat---------gccaataaaaccttt---gaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
|||| | ||| || | | | ||| | || | || ||| | ||| | | | ||| || | | | ||||| || ||| ||||| ||||| || ||||| || ||||| || |||||||| |||||||| ||||||||||| ||||| || | |||||||| || ||||||||||| ||||
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtg----tatatggataggaattattatgccaataaaacctt-tgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
|| | |||| |||| | |||| || | || | ||| || | ||||| | | | | || | |||| ||||| |||||||| ||||| ||||||||||| ||||| || || || |||||||||||||||||||| || || || ||||| || || || || || || |
------------------gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatt-tactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 7
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaa-acagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
| | || | | || ||| | || | ||| | | || || | ||| | ||| | ||| ||| || ||||| |||||||||||||||||||||||||||||||| || ||||| |||||||||||||| ||||| || ||||| ||||||||||| || ||||| || |
----------------gtctgccgttgataattattttcaagctgtgtttagtatttatgcggtttgatagaaggaaatgttcatg--gacaaatcctccaaatgcagGTGTGGGACTATCAAACCAAAAGTTGTGTCCAGACACTGGAAGGCCACACACACAATGTTTCTGCAGTCTGCTTCCATCCTGAACTTCCCATAATAATAA
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 7
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctt-tgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
|| ||| || | | | || || || | | || | | |||||| || | | || || | |||| | || ||||||| |||||||| ||||||||||||||||| ||||| |||||||| |||||||||||||| ||| | || || || ||||| || || ||||| || |||
------------------gtgtttatctgatgcttattgact--aaatagcttccatttatgtgcattccatttgattactttctgtgattaaattttggtggaacagGTGTGGGACTACCAAACCAAAAGTTGTGTTCAGACACTAGAAGGCCACACACACAATGTTTCTTCAGTCTGTTTCCATCCAGAGCTTCCTATTATTTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
ccttt CT-rich tract
ataggaattattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT