Sequence
atgc intronic sequence ATGC exonic sequencegtgatctttttcaattcccttcaagatctcatttaccagttttctgctttgaactagtttttccttcatgataattggataatatatatttaaaatttaaagtaaatttgcattagtcaatttttttttcttactttacagtaataactaggttctctttatttctcagGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC
Basic information
species | Glycine max |
transcript | GLYMA16G23840.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G23840.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 6
------gtgatctttttcaattccctt--caagatctcatttaccagttttctgctttgaacta-gtttttccttcatgata-attggataatatatatttaaaatttaaagtaaatttgcattagtcaatttt---tttttcttactttacagtaataactaggttctctttatttctca-gGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC
|| |||||| || || | | | | |||| | || || || | | | | ||| | | | ||| | | || || | || || | | | | || ||| || || ||| | | || | || | ||| ||| || || | ||||| |||||||||||||||| ||||| || |||||||||||||| ||||| ||||| ||||| | | ||||| |
gttacaatgccatttttcttttggtttgatatggtttagcttactcatattttgtcttatgcaatatgcagtttgtatgttttagcagctaagccttgacaataaaatatattatatgaagaccatatagtgttgagctttcctcacattagttttgagagcagctgacctgtgttttagGTGGTGTTGTTGCATCTGCTGCATATAAAAAATGGGAGAGAGCTGCCATGGCTGGTGTTTCTTTGGTTGCTGATGCAGCTGAAGAGCTTGAGCGCAACAC---
upper sequence: GLYMA16G23840.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g56234.1 (Oryza sativa), 3'ss of exon 6
-----------gtgatctttttcaattcccttcaagatctcatttaccagttttctgctttgaacta-gtttttccttcatgataattggataatatatatttaa-aatttaaagtaaatttgcattagtcaatttttttttcttacttta-cagtaataactaggttctctttatttctcagGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC
| | ||||| || | | | | ||||| ||| | | || || | | | | || | || || || || || | || | || | | |||| ||||| || | | | | | || | ||| ||| ||| || | |||| |||||||||||||||| | ||| || ||||||||||||||||| || ||||| ||||| | | ||||| |
gtgacactgctttttttttttttggtttcatgtggcacaccctttacttttttcattttatgcgatatgcagtctgtatgtcttagctaaatgtcgataatccaataaattttattatgtgagcttaaagtgtcgaattttccttacaatagttttgagagcagtggacttgtattttagGTGGTGGCATTGCATCTACTGCATATAAAAAATGGGAGAGAGATGCCATGGCTGGTGTTTCTTTAGTCGCTGATGCAGCTGAAGAGCTTGAGCGCAACAC---
upper sequence: GLYMA16G23840.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 7
-----------------------gtgatctttttcaattccct---tcaagatctcatttacca-----gttttctgctttgaactagtttttccttcatgataattggataatatatatttaaaatttaaagtaaatttgcattagtcaatttttttttc-ttactttacagtaataactaggttctctttatttctca-gGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC
|| |||||| || ||| | || ||| ||| | | || ||||| | | |||| |||| | | ||| | || || || | | | | | | || || ||| || | || | ||| || | ||| || | ||| ||| | || || | || || |||||||||||||||| || || || |||||||||||||||||||| ||||| |||||| | | ||||| |
gtgggcgcatgttctctgttagtctgttcttttgttatgacctagccttgcttatcttttgccacacaatctgtgtgatttgagtctcggtgaaatcgttgatgattgaa-actatcaaactatcatgtagaagagctctctagtggtgaacctttgttacattgcattaatgtggatagatggtgacctgtgttttagGTGGTGCTGTTGCATCTGCCGCATATAAAAAATGGGAGAGAGCGGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCGGCTGAGGAGCTCGAGCGCAACAC---
upper sequence: GLYMA16G23840.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G085427_T02 (Zea mays), 3'ss of exon 7
--------gtgatctttttcaattcccttcaagatctcatttaccagttttctgctttgaactagtttttccttcatgataattggataatatatatttaa--aatttaaagtaaatttgcattagtcaatttttttttcttactttacagtaataactaggttctctttatttctca-gGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC
| ||| |||| || | | | | || || | || || | || || | | | | || | | | |||| | | || | | |||| | | ||| || | ||| || | ||| || | ||| || | || || | ||||| ||||| |||||||||| || || || |||||||||||||||||||| ||||| |||||| | | ||||| |
gtgggcacatattctctttccctttgttatgacctagc-cttgcctatcttttg-tcaaaatctgtgtggttagagttttggtgaaattgtttttgattaattatcatgtagaggaccctctctagt-ggtgaatctttgttgcattaatgtggatagctggtgagctatgttttagGTGGCGCTGTTGCATCTGCTGCATATAAGAAATGGGAGAGAGCAGCCATGGCTGGTGTTTCTTTAGTTGCTGATGCAGCTGAGGAGCTCGAGCGCAACAC---
upper sequence: GLYMA16G23840.2 (Glycine max), 3'ss of exon 6
lower sequence: AT2G36960.2 (Arabidopsis thaliana), 3'ss of exon 7
gtgatctttttcaattcccttcaagatctcatttaccagttttctgctttgaactagtttttccttcatgataattggataatatatatttaaaatttaaagtaaatttgcattagtcaatttttttttcttactttacagtaataactaggttctctttatttctcagGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC------------------
| || | |||| | || | | | ||| || ||||||| || | | | || ||||||| | || ||| | |||||| ||| |||| | | ||||| ||||||||| || |||||||| | ||| || ||| | ||||| |||||||| ||||||||||| ||| | |||
----------------------------------------------------------taatcttccatgttgatattagattttatgtt-gctatttaaaa-------gcttgatgtagttccaggttcttacgtgactctaa------gcatctcttcctttttcag---------------cagGTTATAGAAAATGGGAAAAAGCTGCAATAGATGGGGTCTCTCTGGTTGCTGATGCTGCAGAGCATTTGGAACGAACATCAATTGACAAAGATATGGATGA
upper sequence: GLYMA16G23840.2 (Glycine max), 3'ss of exon 6
lower sequence: AT2G36960.3 (Arabidopsis thaliana), 3'ss of exon 7
gtgatctttttcaattcccttcaagatctcatttaccagttttctgctttgaactagtttttccttcatgataattggataatatatatttaaaatttaaagtaaatttgcattagtcaatttttttttcttactttacagtaataactaggttctctttatttctcagGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC---------------
|| || | |||| | || | | | ||| || ||||||| || | | | || ||||||| | || ||| | |||||| ||| |||| | | ||||| ||||||||| || |||||||| | ||| || ||| | ||||| |||||||| ||||||||||| ||| | |||
-------------------------------------------------------ttttaatcttccatgttgatattagattttatgtt-gctatttaaaa-------gcttgatgtagttccaggttcttacgtgactctaa------gcatctcttcctttttcag-
upper sequence: GLYMA16G23840.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0040g01460.t01 (Vitis vinifera), 3'ss of exon 6
gtgatctttttcaattcccttcaagatctcatttaccagttttctgctttgaactagtttttccttcatgataattggataatatatatttaaaatttaaagtaaatttgcattagtcaatttttttttcttactttacagtaataactaggttctctttatttctcagGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC
|||| || | | | | | |||| || | | |||| | ||||| || |||| | || || | | || | | | | ||| | | ||||| | ||||| ||||||| |||||| || |||||||||||||| |||||| | ||||| |||||||| ||||||||||||||| | | |
-------------------------------------------------tgaaataataaacgc------aagttcttacgatatgccattccatggtcaagtg---ccactttagtaaaattttggt-ctggtcttg----------ttgattttggatttctagcagCTGCTGTTTCATCAGCTGCATATAAAAGATGGGAAAAAGCTGCAATTGCTGGGGTTTCTCTGGTTGCTGATGCTGCAGAGCATTTGGAGCGAACAACTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtcaatttttttttcttactttacagtaataactaggttctctttatttctcagGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC
taataac putative branch site (score: 1)
ttctctttatttctc putative PPT
atttttttttcttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatctttttcaattcccttcaagatctcatttaccagttttctgctttgaactagtttttccttcatgataattggataatatatatttaaaatttaaagtaaatttgcattagtcaatttttttttcttactttacagtaataactaggttctctttatttctcagGTACGATTTCAACGGCTGCTTATAAAAAATGGGAGAAGGCTGCAATTGCTGGTGTTTCTTTAGTTGCAGATGCTGCTGAGCATTTGGAGCGAGCTGCAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC