Sequence
atgc intronic sequence ATGC exonic sequencegttgcctcttgtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgatgcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC
Basic information
species | Glycine max |
transcript | GLYMA07G16400.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G16400.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g38270.2 (Oryza sativa), 3'ss of exon 5
gttgcctcttgtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgat--gcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC-------
|| | | ||| ||| | || |||| | | | | | || | | ||| ||||| || ||||||| |||||| || ||||| | || ||||||||||||||||| ||||| || |||||||| ||||| || || ||| | | || || || ||||| |||| ||||
-------------------gtaacttatattgggcgtttactgctgtattctcttcacactcaact---aggttaggtaagcatgctgatcagcgaaatattttctccaaagctt-cagATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACCTTGTGT
upper sequence: GLYMA07G16400.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
gttgcctcttgtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgat--gcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC-
|| | | ||| ||| | || |||| | | | | | || | | ||| ||||| || ||||||| |||||| || ||||| | || ||||||||||||||||| ||||| || |||||||| ||||| || || ||| | | || || || ||||| |||| ||||
-------------------gtaacttatattgggcgtttactgctgtattctcttcacactcaact---aggttaggtaagcatgctgatcagcgaaatattttctccaaagCTT-CAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC
upper sequence: GLYMA07G16400.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
gttgcctcttgtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgatgcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC-------
||| | || || | || | || ||| | ||| | | || | | || |||| | | ||||||| | || ||||| ||||||||||| |||||||| ||||| || ||||| ||||||||| || | | || || || || |||| | |||
-------------------------------gtaacctgcatatgtcattatgacactgaca-tttgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
upper sequence: GLYMA07G16400.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgcctcttgtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgatgcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC-------
|| ||| || | | ||| || ||| |||||| | | | || | | || |||| ||||| ||||||| |||||| ||||| | |||||| | ||||||||||| |||||||| ||||| || |||||||||||||| || | || ||||| ||||| |||||||| ||||
--------gtgaagttgaataa-acgactttttaca---aatccgagatgaagct---gctaccttgtagttgaagattcatttgaggatg-atcatgtttttacggaagttt-cagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT
upper sequence: GLYMA07G16400.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------------------------gttgcctctt-gtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgatgcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC-------
|| | |||| ||||||||| ||||||||||||||||| ||||||| |||| || ||| | | ||| |||||||||||||||||| || ||| |||| |||||||| |||||||||| ||||||||||| |||||||| ||||| |||||||| ||||||||||| |||| |||| || || |||||||| ||||
gtaaattctccatcccctgggtcactgcagcccacacaagccacagttttcaggtgtagcaatttcttctttgtggttacactatatagttttgtaggtcatttgaagtacgaagctatggaagatctttaatgtaaagcaagacacctaat-----------ttaacaaaagtttcagATATGGGACAGGTGTGGGGTTGGGGCTATGGAGGCGAAGGGCAGCTAGGTTTGGGTTCTCGGACAAAGCTGGTGTCTTCTCCTCATCTCATACCTTGCTT
upper sequence: GLYMA07G16400.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S44_203V6.1 (Physcomitrella patens), 3'ss of exon 5
------gttgcctcttgtggttacattat-atagttttgtaggttcaatgaagtatgaa-gataaggatggtttttgatgtaaagcaagacacctgatgcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC-------
| | || ||| || | || | | || |||| | ||||| | | || | | | || || | | || | || | | ||| | | |||||||||| || || ||||||||||||||||||||||| || || || || ||||| | || | ||| ||||||||||| || || || |
gtgagtttagtttcaagtgtttgaccaaccattttccttaagcttcacagggctatgatcgcctatgactatgtaggttggaatgtatgaatatttctgaactcttgtttctctggggaa--cagATGTGGGTCACGTTTGGGGTTGGGGTTATGGAGGTGAGGGCCAACTTGGGTTGGGCACCCGCATGCGGATTGTATCATCCCCGCAACTCATTCCGTGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggatggtttttgatgtaaagcaagacacctgatgcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC
acctgat putative branch site (score: 4)
tttttacc putative PPT
atatttttaccaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgcctcttgtggttacattatatagttttgtaggttcaatgaagtatgaagataaggatggtttttgatgtaaagcaagacacctgatgcatcatatttttaccaaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGTTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGAGTAAAGATGGTATCATCCCCTCATCTTATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG