Sequence
atgc intronic sequence ATGC exonic sequence...tgcaaaattaatattttttcttcaagttgttatacacatcatttattttgattttgctttcagaagtggttctttattaattttcttccgttgctttcagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
Basic information
| species | Glycine max |
| transcript | GLYMA04G06930.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
-----tgcaaaattaatattttttcttcaagttgttatacacatcattt-attttgattttgctttcagaagt--ggttctt------tattaattttcttccgttgcttt-------cagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
| | ||| || | ||| | || | | ||| ||||||| |||| | | | ||| ||| | || | || | ||| | || || || ||||| | ||||| || || |||||| |||| |||||||| ||||| || || |||| ||||| |||||||| ||||||||||||||||||| | | |
gtaatttcctaatatttacctgttcattaaaat-tcatagggatcatttgatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
upper sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G882708_T03 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------tgcaaaattaatattttttcttcaagttgttatacacatcatttattttgattttgcttt------cagaagtggttctttattaattttcttccgttgctttcagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
| |||| || | | | ||| | || | ||| | || | |||| | | || || || || || || | |||||| |||| || || || |||||| |||| |||||||| ||||| |||||| | || |||||||||||||| ||||||||||||||||||| || | |
gtaaactttgcatgttaatttgtaattcctggggactagaaatgttcatctgaataacatttgtttctcaaaaactactgacatatgttcctgaaagcctagatttcaatcataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG
upper sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G882708_T01 (Zea mays), 3'ss of exon 1
tgcaaaattaatat-tttttcttcaagttgttatacacatcatttattt--tgattttgctttcagaagtggttctttattaattttcttccgttgctttcagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
| | | | || | || || ||| || ||||| | | ||| | | | || || || || || || | |||||| |||| || || || |||||| |||| |||||||| ||||| |||||| | || |||||||||||||| ||||||||||||||||||| || | |
---actactgacatatgttcctgaaagcctagatttcaatcataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG
upper sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------------tgcaaaattaatattttttcttcaagttgttatacacatcatttattttgattttgcttt------cagaagtggttctttattaattttcttccgttgctttcagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
| |||| || | | | | || || || | ||| | | | |||| | | || || || || || | || | |||||| |||| || || || |||||| |||| |||||||| ||||| || || | || ||||||||||| || ||||||||||||||||||| || | |
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG
upper sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
tgcaaaattaatattttttcttcaagttgttatacacatcatt-tattttgattttgctttcagaagtggttctttattaattttcttccgttgctttcagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
|| | ||| | | || | | || | || | | | | || | |||||| || ||| ||| | | ||| || || |||||| | ||||| ||||| |||||||| ||||||||||| |||||||| || |||| |||||||||||||| ||||||||||||||||||||| || |||
tgtcttttagggattctattttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagagtacttgattg-tgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgattttgctttcagaagtggttctttattaattttcttccgttgctttcagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
tattaat putative branch site (score: 2)
ttttcttccgttgctt CT-rich tract
ttctttattaattttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcaaaattaatattttttcttcaagttgttatacacatcatttattttgattttgctttcagaagtggttctttattaattttcttccgttgctttcagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
- -aaaattaa
- - - - - - - - - -cttcaag
- - - - - - - - - - - - - - - - - cacatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtggtt
