Sequence
atgc intronic sequence ATGC exonic sequencegtaaatattggattaaattaaattcctaagcatggcttctttactatgaataagctatctattttattgttttgcattaccatgactctaatattaaaatttaaactgtatgagattttggactatgttgtcagGCAGGAGTTGAAAGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACTTAGAGCGTTACTTTGAGAA
Basic information
species | Glycine max |
transcript | GLYMA04G38370.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38370.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 3
gtaaatattggattaaatt------aaattcctaagcatggct-tctttactatgaataagctatctattttattgttttgcattaccatgactctaatattaaaatt-taaactgtatgagatt----ttggactatgttgtcagGCAGGAGTTGAAAGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACTTAGAGCGTTACTTTGAGAA
||||||| ||| || || | |||| | | | | ||| | | | ||| | || | ||| || || | | |||| || ||| ||||| | | ||| | | |||| | ||||| || | ||||| | || || |||| ||||||||||||| ||||||||||| ||||||| ||| || || |||||||| ||
gtaaataatggttttgtgctccccagtcttttctatcatgcccattataaatattatcctaccagatatgtatccaggttactgtactataacctttcttttaatgttgtaagttgtatcaagtgctaattgtttggttctaacagGGAAGAGTTAGAAATCTTTTCAAAAGAAGTTGTTCGATTTGGAAATCGTTGCAAGAATCCTCAATGGCACAGCTTGGACCGCTACTTTGAAAA
upper sequence: GLYMA04G38370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 3
--------------------gtaaatattggattaaattaaattcctaagcatggcttctttactatgaataagctatctattttattgttttgcattaccatgactcta---atattaaaat---ttaaactgtatgagattttggactatgttgtcagGCAGGAGTTGAAAGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACTTAGAGCGTTACTTTGAGAA
| | | || | || | || | | | | | ||| || ||| | | || | | | | | | || | | || | || | | | ||| |||| | |||| | ||||||||||| || ||| || || |||| ||||||||||||| ||| ||||||||||||||||||| || || |||||||| ||
gttagtgaataatctctgattctttttataaactataacaattgtctgaaccatttgtttattttatttatctagcatcaacctggttatatagaagaaatgtacttcaacttgtttttatatgcttgtagttacctgaagtttttatttggtccaacagGGAAGAGTTGAAAGTGTTCTCTACAGAAGTTGTTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCACAACTTGGACCGCTACTTTGATAA
upper sequence: GLYMA04G38370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
----------------------------gtaaatattggattaaattaaattcctaagcatggcttctttactatga-ataagctatctattttattgttttgcattaccatgactctaatattaaaatttaaactgtatgagattttggactatgttgtcagGCAGGAGTTGAAAGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACTTAGAGCGTTACTTTGAGAA
|||| ||| || ||| |||| | | | | || | | | || || ||| ||| | | | | | | | | | | ||||| ||| | || || || | || ||||| | |||| |||| ||| | | ||||| ||||| ||||||||||||| ||| ||||||||||||| ||||| || | |||||||| ||
gtttgtgcttgtgttcacttcttatcatgtaattat-ggcctaatttaattatccattcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtagtgtgccttttatttttatattgaaaacaataccttaa------ttagttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA
upper sequence: GLYMA04G38370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G077621_T01 (Zea mays), 3'ss of exon 2
------------gtaaatattggattaaat--taaattcctaagcatggcttctttactatgaat---aagctatctattttat-tgttttgcattaccatgactctaatattaaaatttaaa-ctgtatgagattttggactatgttgtcagGCAGGAGTTGAAAGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACTTAGAGCGTTACTTTGAGAA
|| | | || | | | | ||||| | | || || | | |||| | | | | || | || || || | || || | ||| ||| | || | || | || ||||| | ||||| |||| || | | ||||| ||||| |||||||| |||| ||| ||||||||||||| ||||| || || |||||||| ||
gtttgtgcttgtgttcacttcttatcatgtaattatggcctaatttatccatgcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtattgtgccttttatttttatattgaaaacaataccttaatt-agttaattccatcagGGAAGAGTTAGAAGTATTCACAAAAGAGGTCATTCGCTTTGGAAACCGTTGCAAGGATCCTCAGTGGCATAACTTGGACCGCTACTTTGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatgactctaatattaaaatttaaactgtatgagattttggactatgttgtcagGCAGGAGTTGAAAGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACTTAGAGCGTTACTTTGAGAA
ctctaat putative branch site (score: 3)
taatattaaaatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatattggattaaattaaattcctaagcatggcttctttactatgaataagctatctattttattgttttgcattaccatgactctaatattaaaatttaaactgtatgagattttggactatgttgtcagGCAGGAGTTGAAAGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACTTAGAGCGTTACTTTGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA