Sequence
atgc intronic sequence ATGC exonic sequence...attgcatattcgttactcattagtactaacttcccatgtgctgaggtcttcacattttaataatttaacttaggacttttctttgtgtgaaatgcaacagTGCTGGCATCTCAATAGGCAGTGAGATGTCTGGTGGGGTATCCAACGTCCTGGTGGAGAACATTCTTGTATGGGAATCAAGGCGTGCCATGAGAATCAAG
Basic information
species | Glycine max |
transcript | GLYMA09G08270.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g54030.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------------------------------attgcatattcgttactca-ttagtactaacttcccatgtgctgaggtcttcacattttaataatttaacttaggacttt--tctttgtgtgaaatgcaacagTGCTGGCATCTCAATAGGCAGTGAGATGTCTGGTGGGGTATCCAACGTCCTGGTGGAGAACATTCTTGTATGGGAATCAAGGCGTGCCATGAGAATCAAG
|| | | || | | |||| | |||||| | | | | | | || | || | | | ||| | |||| | ||||||||| || ||||| ||||||||||||||||||||| | | || || |||||| | | | | ||||| ||| |||| | ||||||| |||
gtaacagttgagtcatttttggctgcattgcttcatctaaaatatttctttgcatatctttttcaaatcctgctcaagataaaatggtatgagaaagaaactattaaattaggattaacttttaagttcttttgaattgaatatag-agtattacaggtaaggtttacaacagttgtcttggtgtgtgcagTGCTGGAATTTCAATTGGCAGTGAGATGTCTGGTGGGATTGCAAATGTTACAGTGGAGGATGTCCGCATTTGGGAGTCACGGCGAGGTTTGAGAATAAAG
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G348602_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------attgcatattcgttactcattagtactaacttccca-tgtgctgag-gtcttcacattttaataatttaacttaggacttttctttgtgtgaaatgcaacagTGCTGGCATCTCAATAGGCAGTGAGATGTCTGGTGGGGTATCCAACGTCCTGGTGGAGAACATTCTTGTATGGGAATCAAGGCGTGCCATGAGAATCAAG
| | || |||| |||| ||| || | | | || || | | | ||| ||| |||| ||| | | | | ||||||||| || ||||||||||||||||||||||| || || | || || |||||||| | | | |||||||||||| | | |||| || |||
gtgagaattgagatatgttggctacattgtgtgtctacaataatctacttttgtgcatagtcctttgaagtcaaacctcaagagtagtaaattacgactatggtgtgtattgctgaacattatcaatcaggcttac-actatctaccctatct--ttgtgcagTGCTGGAATTTCAATAGGCAGTGAGATGTCTGGCGGAGTTGCAAATGTTACTGTGGAGAATGTGCGCATCTGGGAATCAAGGAGAGGTGTGAGGATAAAG
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 4
attgcatattcgttactcattagtactaacttcccatgtgctgaggtcttcacattttaataatttaacttaggacttttctttgtgtgaaatgcaacagTGCTGGCATCTCAATAGGCAGTGAGATGTCTGGTGGGGTATCCAACGTCCTGGTGGAGAACATTCTTGTATGGGAATCAAGGCGTGCCATGAGAATCAAG
| | | | ||| || | | | | || || | | | || || | | || |||| ||| |||| ||||| || |||||||| ||||||||||||||||| || || || || || ||||| ||||| | ||| || |||||| | || || ||
---------------gtaagagagaattgctttccctaatcaatgttgatctaataatcaacgtgtacctaaag-----cctctgtgcaaaa----acagCGCTGGTATATCAATAGGAAGTGAGATGTCTGGTGGTGTCTCGAATATCACAGTCGAGAATATTCTGATTTGGAGCTCCCGGCGTGGAGTTAGGATTAAA
upper sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 4
----attgcatattcgttactcattagtac-taacttcccatgtgctgaggtcttcacattttaataatttaacttaggacttttctttgtgtgaaatgcaacagTGCTGGCATCTCAATAGGCAGTGAGATGTCTGGTGGGGTATCCAACGTCCTGGTGGAGAACATTCTTGTATGGGAATCAAGGCGTGCCATGAGAATCAAG
| | | | || | | | ||||| | | | || |||| | | ||||| || | || | || | || |||||||||||| | |||||||||||||| ||||||||||| || || || ||| ||||| ||| ||||||| ||| | ||||||||||| | | ||||||
gtcttcaatgagtctatcccccccccataggtgatgtagcatgtagtaaa--ttgtgtatcttaagattgtaactgagtatgttggctggttt---atccaacagTGCTGGTGTATCAATAGGCAGTGAAATGTCTGGTGGTGTCTCAAATGTCACAGTGGAAAACCTTCTTGTTTGGAACTCAAGGCGTGCTGTTCGGATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttcacattttaataatttaacttaggacttttctttgtgtgaaatgcaacagTGCTGGCATCTCAATAGGCAGTGAGATGTCTGGTGGGGTATCCAACGTCCTGGTGGAGAACATTCTTGTATGGGAATCAAGGCGTGCCATGAGAATCAAG
atttaac putative branch site (score: 3)
attttaataatttaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgcatattcgttactcattagtactaacttcccatgtgctgaggtcttcacattttaataatttaacttaggacttttctttgtgtgaaatgcaacagTGCTGGCATCTCAATAGGCAGTGAGATGTCTGGTGGGGTATCCAACGTCCTGGTGGAGAACATTCTTGTATGGGAATCAAGGCGTGCCATGAGAATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- tgcatat
- - - - - - - - - - - - - - -cttccca
- - - - - - - - - - - - - - - - - - - -gctgagg
- - - - - - - - - - - - - - - - - - - - - - - tcttcac