Sequence
atgc intronic sequence ATGC exonic sequencegtacctaactatcccaactgtgtggtttcttatcttttattcacgaacttgtattttcttttgcttttgtatttgttaactggtattctacatattgttacctttcccgattaagcaaatgctatctccattttctttttgataacagCTTTCTCCTCCATGGTTGAGGGAAATAATGAGGAGATTTCTACATCTGAACTATTTGGTGGAGCACGAATCCATTACATTTTTCAATCTATCTTTGTCAG
Basic information
species | Glycine max |
transcript | GLYMA04G16340.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 8
gtacctaactatcccaactgtgtggtttcttatcttttattcacgaacttgtattttcttttgcttttgtatttgttaactggtattctacatattgttacctttcccgattaagcaaatgctatctccattttctttttgataacagCTTTCTCCTCCATGGTTGAGGGAAATAATGAGGAGATTTCTACATCTGAACTATTTGGTGGAGCACGAATCCATTACATTTTTCAATCTATCTTTGTCAG
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---------------------gcgacttataatatgaaacggagggagt-gtgtctatt----cttttgt-----ttaagctgtatgtgataaattgtgccattttaagttgaaaca-----------------tttttatgttatagCTTTCTCCTCAATGGTGGAGGGAAAAAATGAGGACATATCAACAATTGAGCTTTGTGGTGGAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAA
upper sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g31190.1 (Oryza sativa), 3'ss of exon 8
gtacctaactatcccaactgtgtggtttcttatcttttattcacgaacttgtattttcttttgcttttgtatttgttaactggtattctacatattgttacctttcccgattaagcaaatgctatctccattttctttttgataacagCTTTCTCCTCCATGGTTGAGGGAAATAATGAGGAGATTTCTACATCTGAACTATTTGGTGGAGCACGAATCCATTACATTTTTCAATCTATCTTTGTCAG---
| || ||| | | || ||| | | || || || || | | | | | || | || || | | | | ||| | |||| ||| | ||| || || |||||||| || || || ||| | | | || ||| |||||||| |||||||||| ||||||| ||||||||||| || || |||||||
----------------------------------tgttgctcatgtgc--atagtttttcgtcctcttcaatctgccactttgatgattccctaa-gctatattcttctaatgtgattatgttttctctgtttcc-----------agCCTTTTCTTCCATGGTGGAAGGGAAAAATAAAGTG---TCAACAGATGAACTATCTGGTGGAGCAAGAATCCACTACATTTTTCAGTCAATTTTTGTCAAGAG
upper sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 8
gtacctaactatcccaactgtgtggtttcttatcttttattcacgaacttgtattt-tcttttgcttttgtatttgttaactggtattctac-atattgttacctttcccgattaagcaa-atgctatctccattttctttttgataacagCTTTCTCCTCCATGGTTGAGGGAAATAATGAGGAGATTTCTACATCTGAACTATTTGGTGGAGCACGAATCCATTACATTTTTCAATCTATCTTTGTCAG
|| | | | ||||| || | ||| | ||||| | | ||| || || || | | | | |||| | ||| || |||| | | || | | || | |||||||||||| ||||| || ||||| ||||| || || || ||| |||||| | |||||||||| | |||||||||||||| || |||||||||||||
-------------gtaaatattgaactatgacacttttgttaaggaaactatatttatgccctataattgctagaattgcctattactttcctgtgttgt-gcttttatattttgagcattaaataacctgtgtatactgt--------agCTTTCTCCTCAATGGTGGAAGGAAAAAATGAAGATATATCGACAATTGAACTCTCTGGTGGAGCAAGGATCCATTACATTTTCCAGTCTATCTTTGTCAA
upper sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 8
gtacctaactatcccaactgtgtggtttcttatcttttattcacgaacttgtattttcttttgcttttgtatttgttaactggta-ttctacatattgttacctttcccgattaagcaaatgctatctccattttctttttgataacagCTTTCTCCTCCATGGTTGAGGGAAATAATGAGGAGATTTCTACATCTGAACTATTTGGTGGAGCACGAATCCATTACATTTTTCAATCTATCTTTGTCAG
|| | || | | | |||| | | ||| | | | | | | || || || || || | | | ||| ||| | | |||| | || | | || | |||||| || || ||||| || ||||| ||||| || || || ||| ||||||| | ||||||||| | |||||||||||||| || |||||||||||||
-------------gtaaatatgaaccatgtcacttttt-ctaaggaaactatgtgtgccccaataatagttagaattgcctattactttcatgtgtctttatatttttaaac--attaaata--acctatgtatactgt--------agCTTTTTCGTCAATGGTGGAAGGAAAAAATGAAGATATATCGACAACTGAACTTTCTGGTGGAGCGAGGATCCATTACATTTTCCAGTCTATCTTTGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgttacctttcccgattaagcaaatgctatctccattttctttttgataacagCTTTCTCCTCCATGGTTGAGGGAAATAATGAGGAGATTTCTACATCTGAACTATTTGGTGGAGCACGAATCCATTACATTTTTCAATCTATCTTTGTCAG
ttttgat putative branch site (score: 4)
tgctatctccattttc CT-rich tract
attttctttttgataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctaactatcccaactgtgtggtttcttatcttttattcacgaacttgtattttcttttgcttttgtatttgttaactggtattctacatattgttacctttcccgattaagcaaatgctatctccattttctttttgataacagCTTTCTCCTCCATGGTTGAGGGAAATAATGAGGAGATTTCTACATCTGAACTATTTGGTGGAGCACGAATCCATTACATTTTTCAATCTATCTTTGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA