Sequence
atgc intronic sequence ATGC exonic sequenceggtgcgctcttagtttttatgttttgagttactgttctatccgagaatttatttatttatttgatgttgttgggtattgcaatgcaGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG
Basic information
species | Glycine max |
transcript | GLYMA18G45010.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 3'ss of exon 1
--------ggtgcgctcttagtttttatgt---tttgagttactgttctatccgagaatttatttatttatttgatgttgttgg--gtattgcaatgcaGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG
| | || || || | ||| | | || | | | | | || | | | | || | ||| |||||| || ||||| || ||||||||||||||||| | |||||||| |||||||| | |||| |||||||| ||||||
aacatataaatccatctttcaattgcatatctatttttgcttgtgcaatgattgccatgtaagcatttcaatacacactaaaggaagggttgttgtgcagGTTTCTTTGTCACAATTTGGATTGCTGCTGTAATGTTCAAGTCAAATGATATATTGCGGAAGCAAACTGCTTTGAAG
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G890843_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------ggtgcgctcttagtttttatgttttgagttactgt---tctatccgagaatttat-ttatttatttgatgttgttgggtattgcaatgcaGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG
| | || | | ||| |||| || ||| | | | | |||| | || || | | | | ||| | | |||| || |||||||| |||||||||||||| ||| | ||||||||||||||||| || | || || ||||| |||||
gtggtgctctcatttcccttgtcaacagagcgcaaattcatatgtacatgaccaacttgatgcttagaacctagggtcacactatttgcaaattgaagtaatgtagatgtgtgagggaatgcaggctaattttcttcttcttttgaattgttttgcacagGTTTCTTTGTGACAATTTGGATTGCTGCGGTGATGTTCAAGTCCAATGATATCCTGCGTAAGCAGACTGCTCTGAAG
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G031551_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------ggtgcgctcttagtttttatgttttgagttactgttc-tatccgagaatttatttatttatttgatgttgttgggtattgcaatgcaGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG-----------------------
| | || ||| ||| | |||| || ||| | | | | | | | | ||||| | | ||| |||| | |||| || |||||||| |||||||||||||| ||| | ||||||||||| ||||| || | || || ||||| |||||
gtgttcctcacttatcttccttttcaatagagcagcaaattgatatgtacatgaccaacttgatgcttagaacataggttcacagtatttgcggattgaagtaatgtggacgtgtggggaatgttgtctaaatttgttttggtt---tatttcg-cacagGTTTCTTTGTGACAATTTGGATTGCTGCGGTGATGTTCAAGTCCAACGATATCCTGTGTAAGCAGACTGCTCTGAAGATTGGTGATTGTTTTGTTGAACT
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G064139_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------ggtgcgctcttagtttttatgttttgagttactgttc-tatccgagaatttatttatttatttgatgttgttgggtattgcaatgcaGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG
| | || ||| ||| | |||| || ||| | | | | | | | | ||||| | | ||| |||| | ||| || |||||||| |||||||||||||| ||| | ||||||||||| ||||| || | || || ||||| |||||
gtgttcctcacttatcttccttttcaacagagcagcaaattgatatgtacatgaccaacttgatgcttagaacataggttcacagtatttgcgaattgaagtaatgtggacgtgtggggaatgttgtctaaatttgttttggtt---tatttcg-catagGTTTCTTTGTGACAATTTGGATTGCTGCGGTGATGTTCAAGTCCAACGATATCCTGTGTAAGCAGACTGCTCTGAAG
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G141216_T02 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------ggtgcgctcttagtttttatgttttgagttactgttc-tatccgagaatttatttatttatttgatgttgttgggtattgcaatgcaGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG
| | || ||| || | |||| || ||| | | | | | | | | ||||| | | ||| |||| | |||| || |||||||| |||||||||||||| ||| | ||||||||||| ||||| || | || || ||||| |||||
gtgttcctcacttatcttccttttcaacagagcagcaaattgatatgtacatgaccaacttgatgcttagaacataggttcacagtagttgcgaattgaagtaatgtggacgtgtggggaatgttgtctaaatttgttttggtt---tatttcg-cacagGTTTCTTTGTGACAATTTGGATTGCTGCGGTGATGTTCAAGTCCAACGATATCCTGTGTAAGCAGACTGCTCTGAAG
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G01960.1 (Arabidopsis thaliana), 3'ss of exon 2
ggtgcgctcttagtttttatgttttgagttactgttctatccgagaatttatttat-ttatttgatgttgttg---ggtattgcaatg-caGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG
| || || ||| | | | ||| | || || |||| | | ||||||| || | ||| | | ||||||| ||||| ||||||||||||||||||| | |||||||| ||||||||||| | ||| ||||| || ||||||
------gtactatttcatatctctctctctcgtgtcttttctgatgatttcctcctgctatttgacttttcctcctgctatctctctctcagGGTTCTTTGTCGCCATTTGGATTGCTGCTGTCATGTTCAAGTCAAATGATATTCTCAAGAAGCAAACAGCTTTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttctatccgagaatttatttatttatttgatgttgttgggtattgcaatgcaGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG
atttgat putative branch site (score: 5)
agaatttatttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtgcgctcttagtttttatgttttgagttactgttctatccgagaatttatttatttatttgatgttgttgggtattgcaatgcaGGGTTTTTTGTGACCATTTGGATTGCTGCTGTGCTTTTCAAGTCCAATGATATTCTAAGGAAACAAACTGCGTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG