Sequence
atgc intronic sequence ATGC exonic sequence...agggagtattttaacatacatttaaataattttgtccctaatactttgtttttctttttctcctagctaactgattgcttggaacctttgtcttttgtagTTTTTACCGCAAGACAGGGTCTGTGAGTTTGCAAAGTTAACTCCTGTTCAACTTCTGGAAGAGACCGAAAAGGCTGTTGGTGATCCACAGCTTCCAGAGC
Basic information
species | Glycine max |
transcript | GLYMA20G34020.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g51790.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------agggagtattttaacatacatttaaataattttgtccctaatactttgtttttctttttctcctagctaactgattgcttggaacctttgtcttttgtagTTTTTACCGCAAGACAGGGTCTGTGAGTTTGCAAAGTTAACTCCTGTTCAACTTCTGGAAGAGACCGAAAAGGCTGTTGGTGATCCACAGCTTCCAGAGC
|| || || || | | | || || | |||| | | | | | | | | ||| |||||| || | | ||||| | || |||||| | || ||||| ||||| ||||| || ||| | ||| | ||||||||||| |||||||||||||| ||||| | || || |
gtgcacctccagtccattttagattcagctcttttacatgatccattccttatcattttcctttgcatgccatgatattgta-atccagaggagccactcacttacccttttatcgtgaatctattcctgatttctg-ttgcttttgtgctcaactctgttcagTTTCTTCCTCAAGACCGAGTATGTGAATTTGCGAAGTTGACACCTATCCAATTACTGGAAGAGACTGAAAAGGCTGTTGGAGATCCTAATCTACCTATCC
upper sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G440916_T02 (Zea mays), 3'ss of exon 3
------------------------------------agggagtattttaacatacatttaaataattt-----tgtccctaatactttgtttttctttttctcct------agctaactga-----------ttgcttggaacctttgt------cttttgtagTTTTTACCGCAAGACAGGGTCTGTGAGTTTGCAAAGTTAACTCCTGTTCAACTTCTGGAAGAGACCGAAAAGGCTGTTGGTGATCCACAGCTTCCAGAGC
| || || | || ||||||| || || ||| | ||| | | || ||| |||| | ||||| ||| || | | ||| | | | ||||| || || |||||| |||| | ||| ||||||||| ||| ||| |||||||||| |||||||| ||||||||||||||||| || | | || |
gttggccttaatgtgcagcttcagttcgtgtagatttctgtgtgttgcatcacacatttatatttttactgcatgtttatgatagatcaatgagctgtttgtccttaacaaaagcaactgtggagctttaacttgttttgctgttctgtgcaacacctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAACTTCTAGAAGAGACTGAAAAGGCTGTTGGTGACCCTGATTTACCTATTC
upper sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0064g00180.t01 (Vitis vinifera), 3'ss of exon 4
agggagtattttaacatacatttaaataattttgtccctaatactttgtttttctttttctcctag-ctaactgattgcttggaacctttgtcttttgtagTTTTTACCGCAAGACAGGGTCTGTGAGTTTGCAAAGTTAACTCCTGTTCAACTTCTGGAAGAGACCGAAAAGGCTGTTGGTGATCCACAGCTTCCAGAGC
| ||| || | || | | ||| | | | |||| ||||| || | || | | | | || | || || | ||||| || || ||||||||||||| ||| ||||| |||||||||||||| |||||||| ||||| || |||||||||||||||||||| || || |||| |
cttatgagtttgaatcagggccttcatcttgggctaccttcttgtcttttttccttttcctttcattcttatttttcgttttgggg-ttggtggtggttagTTCTTGCCACAAGACAGGGTCTCTGAATTTGCTAAGTTAACTCCTGTGCAACTTCTAGAAGAAACAGAAAAGGCTGTTGGTGATCCTCAACTACCAGTCC
upper sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ13183 (Selaginella moellendorffii), 3'ss of exon 3
agggagtattttaacatacatttaaataattttgtccctaatactttgtttttctttttctcctagctaactgattgcttggaacctttgtcttttgtagTTTTTACCGCAAGACAGGGTCTGTGAGTTTGCAAAGTTAACTCCTGTTCAACTTCTGGAAGAGACCGAAAAGGCTGTTGGTGATCCACAGCTTCCAGAGC
|||| |||| | | || |||||| || | ||||||||||||||| ||||| || ||||||||||| ||||| | ||||| || | || |||| ||||| ||||| ||||| || |||||| ||||| | | |
-----------------------------------------------gtttggagttttat----ggcgtcttattgctca-----cttcccgtttgtagTTTTTACCACAAGATAGAGTCTGTGAGTTCGCAAAAATGACTCCAATTGAGCTACTGGCGGAGACAGAAAAAGCTGTAGGGGATCCAGAGCTTTCTCACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttttctttttctcctagctaactgattgcttggaacctttgtcttttgtagTTTTTACCGCAAGACAGGGTCTGTGAGTTTGCAAAGTTAACTCCTGTTCAACTTCTGGAAGAGACCGAAAAGGCTGTTGGTGATCCACAGCTTCCAGAGC
cctttgtcttttgt CT-rich tract
tttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agggagtattttaacatacatttaaataattttgtccctaatactttgtttttctttttctcctagctaactgattgcttggaacctttgtcttttgtagTTTTTACCGCAAGACAGGGTCTGTGAGTTTGCAAAGTTAACTCCTGTTCAACTTCTGGAAGAGACCGAAAAGGCTGTTGGTGATCCACAGCTTCCAGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - catacat
- - - - - - - - - - - - - - - - tgtccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctttg