Sequence
atgc intronic sequence ATGC exonic sequence...aagattgattcccattgatgccaatgaacatagaaatgatagtaagtataaaatttactctattgtaagtatttaacaaattccctttctatggtttcagGTTCCCTTCTTCTCACAGATGGATGATCAACTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGAACCTACATTGTTCGTGAGG
Basic information
| species | Glycine max |
| transcript | GLYMA06G30030.1 |
| intron # | 6 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g54760.1 (Oryza sativa), 3'ss of exon 6
aagattgattcccattgatgccaatgaacatagaaatgatagt--aagtataaaatttact---ctattgtaagtatttaacaaattccctttctatggtttcagGTTCCCTTCTTCTCACAGATGGATGATCAACTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGAACCTACATTGTTCGTGAGG
|| || | |||| | | || | | | | | || | | |||| | ||| |||| | || | ||||||||||| |||||||| |||||||| |||||||| |||| || || |||||||| || ||||| || || |||| || || || |||||||| |||||||
----tttttttaaaaaaatgc-atttcttgggcaatttacactacaggtttgccttatacttgaccggtgtgctaattttgtctttacctaccacaatatttcagGTTCCTTTCTTCTCCCAGATGGACAATCAACTTTTGGACGCCATCTGTGAGCGTCTTGTATCATCGTTGTGCACACAGGGCACATACATTGTCCGTGAGG
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g08850.1 (Oryza sativa), 3'ss of exon 6
aagattgattcccattgatgccaatg-aacatagaaat-gatagtaagtataaaatttactctat----tgtaagtatttaacaaattccctttctatggtt--tcagGTTCCCTTCTTCTCACAGATGGATGATCAACTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGAACCTACATTGTTCGTGAGG
|| ||||| |||| | ||| | | |||||| || | | || ||| | | | | ||| | | | | | | |||| || || ||||| |||||||||| ||||||||||||||| || |||||||| || ||||| || ||||||| || || |||||||| ||||| |
--------ttgtcattgccattaatgtagcatttcatttgatagtgagatctcgacattctatatcacttactgattctcaccaatctttcataccgcaatgcattagGTCCCTTTTTTCTCCCAGATGGATGGTCAACTTCTGGATGCCATCTGTGAGCGTCTTGTATCTTCCTTGAGCACAGTGGGCACATACATTGTCCGTGAAG
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G005791_T01 (Zea mays), 3'ss of exon 5
aagattgattcccattgatgccaatgaacatagaaatgatagtaagtataaaatttactctattgtaagtatttaacaaattcc-ctttctatg-----gtttcagGTTCCCTTCTTCTCACAGATGGATGATCAACTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGAACCTACATTGTTCGTGAGG
|| || || || || || | || || || | | | |||| ||| | | |||| | |||| ||| ||| |||||||| || ||||| |||||||||||||| ||||| ||||| || |||||||| || ||||| || ||| |||| |||| || |||||||| |||||||
---atcctttgccccc--tgaaaaagattgcatcgtaaatttgaactacacattgctttctac-ataattgcatggtaaatctcgctttgtatcgcaatgttgcagGTTCCTTTTTTCTCCCAGATGGATGATCAGCTTCTTGATGCCATCTGTGAGCGTCTTGTATCATCACTGTGCACAAAAGGCACATACATTGTCCGTGAGG
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G436583_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------------------------aagattgattcccatt-----gatgccaatgaacatagaaatgatagtaagtataa-aatttactctattgtaagtatt--taacaaattccctttctatg-------gtttcagGTTCCCTTCTTCTCACAGATGGATGATCAACTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGAACCTACATTGTTCGTGAGG
||| | ||||| | || | | | | | ||| | | | | || | | |||| | || | || || ||| | | ||||| || | ||||| |||||||| ||||| ||||| || || ||||| ||||| ||||||||||| ||||||| | || || |||||||| || || |
gtaaatcagcttactacctttgctctctcgtttttttattggtcagcaacagagttagtaacttagtagtgctagttgaattcttatccatttgtgaggtgatcagtggcgcgcctctaacggctagtcttacgaataacctgaccatgagtagtgttacttacttaatcttttatatcgcaatgctgcagGTCCCACTTTTCTCCCAGATGGACGATCAGCTTCTAGACGCCATATGCGAGCGCCTGGTATCGTCCTTGAGCACAGAGGGCACATACATTGTCCGAGAAG
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 7
lower sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 5
aagattgattcccattgatgccaatgaacatagaaatgatagtaagtataaaatttactctattgtaagtatttaacaaattccctttctatggtttcagGTTCCCTTCTTCTCACAGATGGATGATCAACTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGAACCTACATTGTTCGTGAGG
| | | || || | | | || || | || | | | || ||||| | | | | | | ||||| || || ||||| || ||||||||||| || || ||||| ||||||||||| ||||| || |||||| | ||| |||| || ||| |||| ||||| |
-------------------gtaagtttttctattgatt-tgtttatcctacaaatggttcaacttttag--gttaac---tactatcttgaatcatgcagGTCCCATTTTTCTCTCAAATGGATGATCAGCTGCTTGATGCGATATGTGAGCGCCTGGTTTCTTCTCTGTGTACTGAAGGGACTTACCTTGTACGTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtataaaatttactctattgtaagtatttaacaaattccctttctatggtttcagGTTCCCTTCTTCTCACAGATGGATGATCAACTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGAACCTACATTGTTCGTGAGG
atttaac putative branch site (score: 3)
ttccctttctat putative PPT
tattgtaagtatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagattgattcccattgatgccaatgaacatagaaatgatagtaagtataaaatttactctattgtaagtatttaacaaattccctttctatggtttcagGTTCCCTTCTTCTCACAGATGGATGATCAACTTCTGGATGCAATATGTGAGCGGCTGGTATCGTCTCTGAGCACTCAAGGAACCTACATTGTTCGTGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - -tgattcc
- - - - - - - -tgatgcc
- - - - - - - - - - - aatgaac
