Sequence
atgc intronic sequence ATGC exonic sequence...ttacatgtttttaagatttcaccaaaattagtttgaaattgagattatggatatattccagtcatctttaaatttttatggtggtgcaatctgcttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
Basic information
species | Glycine max |
transcript | GLYMA07G03890.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
ttacatgtttttaagatttcaccaaaat-tagtttgaaattgagattatggatatattccagtcatctttaaatttttatggtggtgcaatctgcttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
| || ||| | || | | || || | | | | | | || ||| | || || | | || | | | | | ||| || ||||||||||| | ||||||||||||||| |||| |||||| ||||||| ||||||||||| | |
tggaatatttgttagttgttggcagctcactacttaatacttatgtcagttatg-attgccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 7
-ttacatgtttttaagatttcaccaaaattagtttgaaattgagattatggatatat-tccagtcatctttaaatttttatggtggtgcaatctgcttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
| ||||| | | | | || ||| | |||| || ||| | || || |||||| | || || || |||||||||||| | |||||||| ||||| ||||| |||||| ||||||| ||||||| || | |
ggaaaatgttctatactaatttctgaacgccacttgtgttgctctttataatctcatatcctgagatgttctttgttttatatc--ttgaactattctgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 7
ttacatgtttttaagatttcaccaaaat-tagtttgaaattgagattatggat--atattccagtcatctttaaatttttatggtggtgcaatctgcttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
| || | | | || | | | | ||| | |||| | ||| ||| | || |||||| | || | | | ||| || |||||||||||| | |||||||| ||||| ||||| |||||| ||||||| ||||||| ||| | |
--atatcctatactggttgagtccgagtgctgcttgtgttactctttataatttcataatcctaaggtgttctttgttttatactt-tgaactatttttgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGATCAAGAAG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G000645_T02 (Zea mays), 3'ss of exon 8
---ttacatgtttttaagatttcaccaaaattagtttgaaattgagattatggatatattcc-agtcatctttaaatttttatggtggtgcaatctgcttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
| ||||| | | | | || ||| | |||| || | || | || ||| ||| || | |||| || |||||||||||| | |||||||| ||||| ||||| |||||| ||||||| ||||||| || | |
ctggaaaatgttctatactgatttctgaacgccacttgtgttgctctttataatctcatcctgagatgttctttgttttatatcttgaactattctgt----agACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------------------------------------------------ttacatgtttttaagatttcaccaaaattagtttgaaattgagattatggatatattccagtcatctttaa----atttttatggtggtgcaatctgcttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
| || || ||| | || | | | ||| ||| ||| ||| | ||| | ||| | || | | |||||||||| |||||||||||||| ||||| ||||| ||||| ||||| ||||| || | || ||||||||||
gtattataatattaaacagtttttttttgttggacatattatagtaaacgcttcttgtatgccttggctaaaccatctccactttggcttcattcttgtgcactttttcaccattaccaatttcttttattgtccttccatttgtaatcccaatttcctaatgtctgttttttcttgcagGCTAGAGAACACATTGAATTATGGCCTTGAGAGAGTCTGGGCAATTGGTTACATTAAAAGTTCACGCCG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
-ttacatgtttttaagatttcaccaaaattagt-ttgaaattgagattatggatatattccagtcatctttaaatttttat-----ggtggtgcaatc--tgcttg-----cagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
| || || | | | || | | | |||| ||| ||| | | | || | | |||| || || || | | | | |||| ||||||||||| |||||||||||||| ||||| || ||||||||||||||| | | || |||||||||||
gtaactcgtatgct-gtctgcattggagctgctattgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
ttacatgtttttaagatttcaccaaaattagtttgaaattgagattatggatatattccagtcatctttaaatttttatgg-tggtgcaatctgc-----ttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
| |||| || | | | | | ||| | | | || ||| | |||| ||||| || | | | | ||| | | |||||| |||||||| ||||| |||||||||||||||||||||||| ||||||| |||| |||||||||||
---tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtc---tttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggatatattccagtcatctttaaatttttatggtggtgcaatctgcttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
tctgctt CT-rich tract
tcatctttaaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttacatgtttttaagatttcaccaaaattagtttgaaattgagattatggatatattccagtcatctttaaatttttatggtggtgcaatctgcttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
-tacatgt
- - - - - - - - - -caccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtggt