Sequence
atgc intronic sequence ATGC exonic sequence...ttagggaattgagctatttgtttattagtcaagctataatgaaaaggcaaaaagaaaattttgacattttggttactgctttatttatcaatctgtgcagGGTCCTCAAAAGGTGAAAGTTGGCTCCTCAGACAAAATAGTAACTGCAAAAGATATCATCATTGCTACTGGTTCTGTTCCATTTGTTCCTAAGGGCATTG
Basic information
species | Glycine max |
transcript | GLYMA07G37050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 3
----ttagggaattgagctatttgtttattagtcaagctataatgaaaaggcaaaaagaaaatt-ttgacatt--ttggttactgctttattt--atcaatctgtgcagGGTCCTCAAAAGGTGAAAGTTGGCTCCTCAGACAAAATAGTAACTGCAAAAGATATCATCATTGCTACTGGTTCTGTTCCATTTGTTCCTAAGGGCATTG
|| || | | | | || | || | | || ||| ||| |||||| | || || | || |||| || | | | |||||||| | |||||||| | | ||||||| ||||||||||||||||||| || ||||| |||||||| |
tatcttgtggtagaaaatgcatacaggaatatctcatctgcgaaatatgacataatagaggattgccgacattaatctattcctatcatgatttgatcagGGAAAACAAAAGGTACGGTATGGAAAAGTTGGTTTTCCAGACAAAGAAATCACTGCAAGGAATATCATCATTGCTACTGGATCAGTTCCTTTTGTTCCCA---------
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 3
--------ttagggaattgagctatttgtttattagt-caagctataatgaaaaggcaaaaagaaaatttt----gac----attttggttactgctttatttatcaatctgtgcagGGTCCTCAAAAGGTGAAAGTTGGCTCCTCAGACAAAATAGTAACTGCAAAAGATATCATCATTGCTACTGGTTCTGTTCCATTTGTTCCTAAGGGCATTG---
| || | ||||| || | | | | || || | | | | ||| |||| || || | | | || | || | |||||||||| |||||||| ||| ||| ||||| || | |||||||||||||| |||||||| ||||| ||||| || ||||| ||||| || ||||
gtcagtactcagtagtacgttctattctttcacgtttactaactgtagacaggaacatgatacaaacttttcttaaacgatgatcctaactcatatcaatattttgtatttctgcagGGTCCACAAAAGGTTAAATATGGGA---AGGACAATATTATTACTGCAAAAGATATAATCATTGCCACTGGATCTGTGCCGTTTGTCCCTAAAGGAATTGAAG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 3
ttagggaattgagctatttgtttattagtcaagctataatgaaaaggcaaaaagaaaattttgacattttggttactgctttatttatcaatctgtgcagGGTCCTCAAAAGGTGAAAGTTGGCTCCTCAGACAAAATAGTAACTGCAAAAGATATCATCATTGCTACTGGTTCTGTTCCATTTGTTCCTAAGGGCATTG
| ||| || | | | || | || || || || | || || | || | | || | |||| |||||| | | || || |||||||||||||| ||||| || || ||||||||||||||
-----------------------gtcagtatctctgtgttcttgtctcgtaag---tgtcttctcacaatgcttgtgtttcta-----cagGCACCTCAAAAAGTGAGGTATGGCAAGATCGGCTATGTTGACAAAGTTATCACAGCCAAAGATATCATCATCGCTACCGGATCAGTTCCATTTGTTCCAC---------
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 3
ttagggaattgagctatttgtttattagtcaagctataatgaaaaggcaaaaagaaaattttg-acattttggttactgctttatttatcaatctgtgcagGGTCCTCAAAAGGTGA---------AAGTTGGCTCCTCAGACAAAATAGTAACTGCAAAAGATATCATCATTGCTACTGGTTCTGTTCCATTTGTTCCTAAGGGCATTG
| | || || | | || |||| | | || | | | | |||| |||||||| |||| | | |||| |||||| | | || || |||||||||||||| ||||| || || ||||||||||||||
------------------------------------------gtcagtatcttcaactcttcgtatcttaaggttctcacaatgcttgt--gtttctacagGCACCTCAAAAAGTGAGGTATGGCAAGATCGGCTATGTTGACAAAGTTATCACAGCCAAAGATATCATCATCGCTACCGGATCAGTTCCATTTGTTCCAC--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcaaaaagaaaattttgacattttggttactgctttatttatcaatctgtgcagGGTCCTCAAAAGGTGAAAGTTGGCTCCTCAGACAAAATAGTAACTGCAAAAGATATCATCATTGCTACTGGTTCTGTTCCATTTGTTCCTAAGGGCATTG
ttttgac putative branch site (score: 3)
aaaattttgacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagggaattgagctatttgtttattagtcaagctataatgaaaaggcaaaaagaaaattttgacattttggttactgctttatttatcaatctgtgcagGGTCCTCAAAAGGTGAAAGTTGGCTCCTCAGACAAAATAGTAACTGCAAAAGATATCATCATTGCTACTGGTTCTGTTCCATTTGTTCCTAAGGGCATTG
- - - - - - - - - - - - - - -caagcta
- - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttactg