Sequence
atgc intronic sequence ATGC exonic sequence...ccatgtgtacattgaaggttttgtatggaactaatacatattatccagtgaattgtgcttgtaacttttcttttcaacttcatttttcggttgagtgtagGAAGGGATATGGTATCATCAATGCTGCTGGTGGAATGGGATGGGGTGGAGGAGGTGGAGGAAGAATATCACTTGATTGTTACAGCATACAAGAAGATTTT
Basic information
species | Glycine max |
transcript | GLYMA11G04290.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G04290.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g10380.1 (Oryza sativa), 3'ss of exon 1
ccatgtgtacattgaaggttt--tgtatggaacta-atacatattatccagtgaattgtgcttgtaacttttcttttcaacttcatttttcg--gttgagtgtagGAAGGGATATGGTATCATCAATGCTGCTGGTGGAATGGGATGGGGTGGAGGAGGTGGAGGAAGAATATCACTTGATTGTTACAGCATACAAGAAGATTTT
| | | | || ||| || || ||| |||| | | | | || || || | || | | ||||| | | || | ||| | ||| |||||| || | |||||||||||| | |||||||||||||| ||||| || || ||||| || || ||||||||||| || ||||| |
----cttcccctaggagttttactgaatcaaaccccatactt-ctgttctatgctttctgtggtgatctgtgagatccaactccttattctaatgccattcttagATATGGAAATGGTACGATAAGTGCTGCTGGTGGTAATGGATGGGGTGGAGGTGGTGGTGGGAGGATATCTCTGGACTGTTACAGCATTCAGCAAGATCTG
upper sequence: GLYMA11G04290.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G385413_T01 (Zea mays), 3'ss of exon 1
ccatgtgtacattgaaggttttgtatggaactaatacatattatccagtgaattgtgcttgtaacttttcttttc-aact-tcatttt--tcggttgagtgtagGAAGGGATATGGTATCATCAATGCTGCTGGTGGAATGGGATGGGGTGGAGGAGGTGGAGGAAGAATATCACTTGATTGTTACAGCATACAAGAAGATTTT
| | | ||| | | | | |||| ||| | || | |||| |||| | || |||| |||| | | ||| ||| |||| | || | |||||||||||| | ||||||||||| || || || ||||| ||||| || || ||||||||||| ||| |||||||
--ttccccccctggaaagacacaaacaaaccccataccc--tatgctacatttttttgttgtgacttgtgaaatctaactgtcatcatggcatgccattcttagATCTGGAAATGGCACAATAAGTGCTGCTGGTGGTAATGGATGGGGTGGCGGTGGCGGTGGAAGGATATCTCTGGACTGTTACAGCATTCAACAAGATTTG
upper sequence: GLYMA11G04290.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 2
---ccatgtgtacattgaaggttttgtatggaactaatacatattatccagtgaattgtgcttgtaacttttcttttcaacttcatttttcggttgagtgtagGAAGGGATATGGTATCATCAATGCTGCTGGTGGAATGGGATGGGGTGGAGGAGGTGGAGGAAGAATATCACTTGATTGTTACAGCATACAAGAAGATTTT
|| ||| ||| || || || | | ||||| ||| | || | || || || ||| | || | || || | | ||||||||||| || |||| || ||| | ||||| | ||||||||||||||| || |||||||| || || ||||| ||||||||||||||||||||| |
tacggatttgtcgtgggaatgtgttaaatcaatgttttacatgttaacttgttagttttgtttcgcttcaatctgtctcacct-atcatttgaata--tgtagGAAGGGTTACGGTAAAATATCTGCATCGGGTGGGAGGGGATGGGGTGGAGGTGGCGGAGGAAGGATCTCTCTTGACTGTTACAGCATACAAGAAGATGTC
upper sequence: GLYMA11G04290.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 1
---ccatgtgtacattgaaggttttgtatggaactaatacatattatccagtgaattgtgcttgtaacttttcttttcaacttcatttttcggttgagtgtagGAAGGGATATGGTATCATCAATGCTGCTGGTGGAATGGGATGGGGTGGAGGAGGTGGAGGAAGAATATCACTTGATTGTTACAGCATACAAGAAGATTTT
|| || ||| | || |||| || | | || | | | | | || | | || || | ||| || || ||| | |||||||||||||| | || | ||| || ||||| | |||||||||||||| || || |||||||||||||| |||||||| ||||||||||||||| |
agatgttgcgtccatgacaaattaattatgtaattgtaatctagtggactttctgtggatttttctccctaactattta-cttaatcatttatttggat--agGAAGGGATATGGCACTATAAGTGCAGCAGGTGGTAGTGGATGGGGTGGAGGTGGAGGTGGAAGAATATCACTGGATTGTTATAGCATACAAGAAGATGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtgaattgtgcttgtaacttttcttttcaacttcatttttcggttgagtgtagGAAGGGATATGGTATCATCAATGCTGCTGGTGGAATGGGATGGGGTGGAGGAGGTGGAGGAAGAATATCACTTGATTGTTACAGCATACAAGAAGATTTT
ttgtaac putative branch site (score: 2)
ttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatgtgtacattgaaggttttgtatggaactaatacatattatccagtgaattgtgcttgtaacttttcttttcaacttcatttttcggttgagtgtagGAAGGGATATGGTATCATCAATGCTGCTGGTGGAATGGGATGGGGTGGAGGAGGTGGAGGAAGAATATCACTTGATTGTTACAGCATACAAGAAGATTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- -tgtgtac
- - - - - - - - - - -tgtatgg
- - - - - - - - - - - - - - - - - - - - - -tccagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt