Sequence
atgc intronic sequence ATGC exonic sequence...gaagttagatactttgattttgggtatgggaatccaccaatgtacagtacaagaatcctattttttctgcatctaaattctttcctttatttccttgcagGGTAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA
Basic information
species | Glycine max |
transcript | GLYMA07G40300.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g13820.2 (Oryza sativa), 3'ss of exon 8
-gaagttagatactttgattttgggtatgggaatccaccaatgtacagtacaagaatcctattttttctgcatctaaattctttcctttatttccttgcagGGTAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA
||| | ||| | | || | | | || || | | || | | | | || || || | ||| |||| |||||||||||||||||| |||||||||||||| || || | ||||| || || || || | ||||| ||||||||| | | |||||| || |
gttagtaaagagcttcaaacctactta--gattttaatcataccttcctaaactgcacaagcaattacaataacaatatactgtcttgtataa----atagGGGTCTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGGAAATTCCCAGAGAGAATTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAA
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
gaagttagatactttgattttgggtatgggaatccaccaatgtacagta-caagaatcctattttttctgcatctaaattctttcct-ttatttccttgcagGGTAA-TGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA
||||| | | | | |||||| || || ||| || || || | | || | | | || ||||| | | || |||||||||| ||||||| || ||||| ||||| ||||| | || ||||| || |||||| | ||||| || ||||| || ||||||||||| |
---gttagtga---taagctcaagtatgg---tctttatatataccttaattagtatgtgccaaatgaaatacctgattacaaggctgttattcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G485898_T03 (Zea mays), 3'ss of exon 8
---gaagttagatactttgattttgggtatgggaatccaccaatgtacagtacaagaatcctattttttctgcatctaaattctttcctttatttccttgcagGGTAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA
||| | | | |||| | || | | | | | | || || | | |||| | | |||| | ||||| || ||||| |||||||||||||||||||||||||| || || ||||| | || ||||| ||||| ||| | || | || ||||| || || |||||||| |
ttcaaaggtgtaaa-tttgcccctctctacgaagtttctctttttt-caagactttactga-atttaaaagaccttgcaattttacggtttatgcttatgtagGGTGCCGGTTGGAAAGTTGTTGCTAGTTTTGAGGGAAAGTTTCCAACTAGGATCAAACAACTACCTGTGGAAAAGCATTTTGATATGAAAAATGTCAAAA
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 8
gaagttagatactttgattttgggtatgggaatccaccaatgtacagtacaa---gaatcctattttttctgcatctaaattctttcctttatttccttgcagGGTAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA
| |||| |||| ||| | || | | ||| | | | | | | | ||| || |||| || ||| | ||||| | |||||||||||||||||| ||||||||||| ||||| || ||| | |||||||| ||||| | || ||||| |||||| | |||||||| || |
-gatatagagtttttgtacttgtctgtgttcagtttatgggctgaagtcccttttggagcttggcaaatgtttttctcaaaacttt--ttgattcttgttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGAAATTTCCCCAACCGTATCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAA
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8
gaagttagatactttgattttgggtatgggaatc-caccaatgtacagtacaagaatcctattttttctgcatctaaattctttcctttat-----ttccttgcagGGTAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA
|| | || ||| || ||| || || | | || | | ||| ||| | | || | |||| | || || | ||||| | |||||||||||||||||| ||||||||||| ||||| || || | ||||| | ||||| | || ||||| |||||| | ||||||||||| |
-----aaggtttttgaattgcatgtctggtgattgtgcccgttcat-gtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 8
gaagttagatactttgattttgggtatgggaatccaccaatgtacagtacaa--gaatcctattttttctgcatc--taaattctttcctttatttcctt-gcagGGTAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA
|| | | |||| | | | ||||| | ||| ||||| ||||| | | | ||| || | || || | |||| ||| |||||||| ||||||||||||||||| ||||||||||| ||||| || ||||| |||||||| || ||| | || | ||| ||||| |||||||||||||| |
----ttcta-gcattgactgctatcaaccttgtgcaccattagacattacaacagaatctgttctactgcccattattagctgctgtcataaattttctttgcagGGTAGCGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAACAGGATCAAGCAGCTACCTTTAGATAAACATTTTGATATAAACAATGTCAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtacaagaatcctattttttctgcatctaaattctttcctttatttccttgcagGGTAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA
atctaaa putative branch site (score: 3)
ttctttcctttatttc CT-rich tract
tattttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagttagatactttgattttgggtatgggaatccaccaatgtacagtacaagaatcctattttttctgcatctaaattctttcctttatttccttgcagGGTAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - -gggtatg
- - - - - - - - - - - - - - - - -ccaccaa