Sequence
atgc intronic sequence ATGC exonic sequence...gtcaactgtaataaattcattgtaatagcaaacattcttcttgtgattattttgaggttcgaatgaaatattgactaggttgggttaatgtgttgtgcagAGAAAGCCAAGATAGGGGAGAAAGAGTGGTACTTCTTCTGCCAAAAGGATAGGAAGTACCCAACTGGGATGAGGACCAATAGAGCAACAGAATCTGGGTA
Basic information
species | Glycine max |
transcript | GLYMA19G28520.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G28520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g01470.1 (Oryza sativa), 3'ss of exon 2
gtcaac-tgtaataaattcattgtaatagcaaacattcttcttgtgattattttgaggt---tcgaatgaaatattgactaggttgggttaatgtg---ttgtgcagAGAAAGCCAAGATA---GGGGAGAAAGAGTGGTACTTCTTCTGCCAAAAGGATAGGAAGTACCCAACTGGGATGAGGACCAATAGAGCAACAGAATCTGGGTA
|| ||| | | | | ||| | | | | ||| | | | |||| | | | |||| || || | | || || | || || ||| || ||||| |||||||| |||||||| |||| |||||| |||||| |||||||||| || ||||||||||| || || || || || ||||
gtaaacattctagtattattttgaattgagagaaattatatatataattagggaaatttatatgatatgatatgatgcatgtgaaaagtaaaaataaataaatgtagGGAAGGCGAAGATGAATGGGGAGAAGGAGTGGTATTTCTACTGCCAGAAGGATCGGAAGTACCCGACGGGGATGAGGACGAACAGGGCGACGGAGGCTGG---
upper sequence: GLYMA19G28520.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g29840.1 (Oryza sativa), 3'ss of exon 2
gtcaac--tgtaataaattcattgtaatagcaaacattcttcttgtgattattttgaggttcgaatgaaatattgactaggttgggttaatgtgttgtgcagAGAAAGCCAAGATA---GGGGAGAAAGAGTGGTACTTCTTCTGCCAAAAGGATAGGAAGTACCCAACTGGGATGAGGACCAATAGAGCAACAGAATCTGGGTA
|| ||| || ||| || ||| | ||| | | | | | ||| | ||| ||| |||| | | | || || || || ||| || ||||| |||||||| |||||||| |||| |||||| |||||| ||||||| || || ||||||||||| || || || || || | ||
gtaaacatcatatagtattagtttgaattgaaaaaaattatat-atatatataattagg---gaaatttatatatatgatatgatgtgaaaaaaaaatgtagGGAAGGCGAAGATGAACGGGGAGAAGGAGTGGTATTTCTACTGCCAGAAGGATCGGAAGTATCCGACGGGGATGAGGACGAACAGGGCGACGGAGGCGGG---
upper sequence: GLYMA19G28520.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07640.t01 (Vitis vinifera), 3'ss of exon 1
gtcaactgtaataaattcattgtaatagcaaacattcttcttgtgattattttgaggttcgaatgaaatattgactaggttgggttaatgtgttgtgcagAGAAAGCCAAGATAGGGGAGAAAGAGTGGTACTTCTTCTGCCAAAAGGATAGGAAGTACCCAACTGGGATGAGGACCAATAGAGCAACAGAATCTGGGTA
|| | || | || || | | | | | || | |||| | || | | || | | | || | | |||| |||||||||| ||||| || ||||| || ||||| ||||| ||||| | ||||||||||| || || || ||||| || ||| |||| || |||||||| ||
gtaatctctctctctatctttct--ctgtgagttctttggttttttggatttggtatttggggcgttatttctaatcttttattggacttgattgtacagAGAAAGCAAAGATGGGAGAGAAGGAATGGTATTTCTTTTGCCAGAGAGATAGGAAGTATCCTACAGGCATGAGAACGAATCGAGCTACCGAATCTGGATA
upper sequence: GLYMA19G28520.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S327_64V6.1 (Physcomitrella patens), 3'ss of exon 1
------------gtcaactgtaataaattcat-tgtaatagcaaacattcttc------ttgtgattattttga---ggttcgaatgaaatattgac-taggttgggttaatgtg------ttgtgcagAGAAAGCCAAGATAGGGGAGAAAGAGTGGTACTTCTTCTGCCAAAAGGATAGGAAGTACCCAACTGGGATGAGGACCAATAGAGCAACAGAATCTGGGTA
||| | | |||| || ||| | || || | ||||| || | | | | || ||| ||||| | ||| | || | | |||||||||||| ||| |||||||||| ||||||||||||||| ||| |||| | ||||| || || || ||| | || |||||||| || ||| || ||
gtgacacaaactcccaatccttccagtatcatctggtgtagtgtgctgtcctccgaatttggtgatcatgtgaactgagatggaccgaatcattgaaattagtttcctcggtgggaaatgatcttgcagAGAAAGCGAAGTTAGGGGAGAAGGAGTGGTACTTCTTCAGCCTGCGGGATCGCAAGTATCCGACGGGAATGCGAACAAATAGAGCCACCGAAAAGGGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattttgaggttcgaatgaaatattgactaggttgggttaatgtgttgtgcagAGAAAGCCAAGATAGGGGAGAAAGAGTGGTACTTCTTCTGCCAAAAGGATAGGAAGTACCCAACTGGGATGAGGACCAATAGAGCAACAGAATCTGGGTA
aatgaaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaactgtaataaattcattgtaatagcaaacattcttcttgtgattattttgaggttcgaatgaaatattgactaggttgggttaatgtgttgtgcagAGAAAGCCAAGATAGGGGAGAAAGAGTGGTACTTCTTCTGCCAAAAGGATAGGAAGTACCCAACTGGGATGAGGACCAATAGAGCAACAGAATCTGGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- caactgt
- - - - - - - - - - - - - - caaacat
- - - - - - - - - - - - - - - - - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttggg