Sequence
atgc intronic sequence ATGC exonic sequencegtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttcttttttaaagctgttgcatagttaacaaaattgagccttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
Basic information
species | Glycine max |
transcript | GLYMA13G34560.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttcttttttaaagctgttgcatagttaacaaaattgagccttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
| || | ||| | || | | | | || | ||| | || | | ||||| | ||||| | | | ||||||||||||||||| |||| | || | || || ||||| || |||||||| |||||||||||||||||||| || ||||||
-----------------------gtgagttacagaaa-caatactatgatatcaaacatcctatggtttctta--tcatctaattgtg------aaatttcaaatataatttagGATAAGGAATTGTTTGGTTCAACTATACTCAAAGGATATCACACCAGATGATAAACAGGAGCTTGATGAGGCTCTCCAGAGGGAG
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttcttttttaaagctgttgcatagttaacaaaattgagccttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
| ||| | | | | | | | ||||| | | | || | ||| ||| |||||| |||| ||| | ||| | ||| | || || |||||||| ||||| ||||| ||||||||||||||||| || || |||
-----------------------------gttagtcggcgaaacagcgcgatttgctcacaccacatgatgtagtttctagtctctaatctcgattgtaacattcttatttcagGATTCGGAACTGTCTGGTTCAGCTTTATTCAAAGGATATCACTCCAGATGACAAGCAAGAGCTTGATGAGGCTCTCCAGAGAGAG
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttcttttttaaagctgttgcatagttaacaaaattgagccttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
| ||| | | || || | || | | | | ||| || || | ||| | | || | | | ||||||| | || ||||| |||| | || | ||||| |||||||| |||||||||||||| |||||||||||||| ||||| |||
-----------------------------gttagtttgccaaccagtgcattgtagttgacatgcacaacttcgtt--cagcctttaatctt--gatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAG
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttcttttttaaagctgttgcatagttaacaaaattgagccttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG---------------
| ||| | | || || | || | | | | ||| || || | ||| | | || | | | ||||||| | || ||||| |||| | || | ||||| |||||||| |||||||||||||| |||||||||||||| ||||| |||
-----------------------------gttagtttgccaaccagtgcattgtagttgacatgcacaacttcgtt--cagcctttaatctt--gatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttcttttttaaagctgttgcatagttaacaaaattgagccttatggttttcatctgcat-tgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
|| | ||| || ||| |||| | || | | | || | | | | |||||| | | || ||| ||| ||| || || ||||||||||| || |||||| ||||| | ||||| || ||||||||||| ||||| || ||||| |||||||| || || ||||| |||
--atgaaaagaaaagtaatatatttctcgagtcatgttgaaccatatgttatatgtgccat--ttgttgcct-----------tagattcttcacatttgcatttgaatgtgcagGATAAGAAACTGTTTAACTCAACTTTATGCAAAGGACATCACTCCAGATGAGAAACAGGAACTTGATGAAGCACTTCAAAGAGAG
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 2
gtttgttacaaaatatagtatttttcagcttcagtatt-cacttttgtattttcttttttaaagctgttgcatagttaacaaaattgagccttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
|||||| | |||| | | || | | | | | | |||| | | | ||||||| | || | ||||| ||| ||| | |||||| |||| |||||| | || || |||||||||||||| |||||||||||||||||||| ||||||||||||||||| || |||
gtttgtaatcaaat-tcctgcccttttgttcttgcactataattttttctctcctttttttcacctct----------------------cttat----ttcttctact---cagGATCCGGAACTGTTTAGCCCAGTTATATGCCAAAGACATTACTCCTGATGATAAGCAGGAACTTGATGAGGCTCTACAGAGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagctgttgcatagttaacaaaattgagccttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
agttaac putative branch site (score: 3)
ttttcatct putative PPT
atagttaacaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttcttttttaaagctgttgcatagttaacaaaattgagccttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT