Sequence
atgc intronic sequence ATGC exonic sequence...ttagaaaaagaaataaaaacattttttcctcatcataatattaatatcacattattttagttgttcttcacaaataccatttcttcttgtatatttgcagGAGGTTATGATAAAGAAGAAAAAGCAGCTAGAGCGTATGATTTGGCGGCACTGAAATACTGGGGAGCAACGACAACAACAACAAATTTTCCA
Basic information
species | Glycine max |
transcript | GLYMA10G31440.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G31440.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g40070.1 (Oryza sativa), 3'ss of exon 3
-----ttagaaaaagaaataaaaacattttttcctcatcataatattaatatcacattattttagttgttcttcacaaataccat-ttcttcttgtatatttgcagGAGGTTATGATAAAGAAGAAAAAGCAGCTAGAGCGTATGATTTGGCGGCACTGAAATACTGGGGAGCAACGACAACAACAACAAATTTTCCA
| | | | ||| | || | | | | | | ||| | ||| ||||| || ||||| | || | | | | |||| || ||||| || || || |||||||| ||||| ||||||||||| || ||||| || ||||| |||| ||||||||||||||| |||
tttatcttggtatgcatgcaaacgccttcagtttttttttcattgtatata----actatattagtga--ctgcacaatcattatacttgtatcacgactactcagGTGGCTATGACAAGGAGGATAAAGCAGCGAGAGCTTATGATTTGGCAGCTCTGAAGTATTGGGGCACAAC---AACAACAACAAATTTCCCA
upper sequence: GLYMA10G31440.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G17430.1 (Arabidopsis thaliana), 3'ss of exon 4
ttagaaaaagaaataaaaacatt-ttttcctcatcataatattaatatcacattattttagttgttcttcacaaataccatttcttcttgtatat----ttgcagGAGGTTATGATAAAGAAGAAAAAGCAGCTAGAGCGTATGATTTGGCGGCACTGAAATACTGGGGAGCAACGACAACAACAACAAATTTTCCA
||| | | |||| | | | || ||||| | |||| | | |||| |||| | || || | ||| | | ||||||||||||| |||||||||||||||||||| || || ||||| || ||||| || || |||||| | || || || || || || ||
------------gtaagttcttgattttaagctataaattaataatagatgactattaaatctattctaagcaaaatataattgttgtgttatctgatcctacagGAGGTTATGACAAAGAAGAAAAAGCAGCTAGGGCTTACGATTTAGCCGCACTAAAGTATTGGGGAACCACCACTACTAC--TAACTTCCCC-
upper sequence: GLYMA10G31440.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------------------------------------------------------------------ttagaaaaagaaataaaaac----attttttcctcatcataatattaatatcacattattttagttgttcttcacaaataccatttcttcttgtatatttgcagGAGGTTATGATAAAGAAGAAAAAGCAGCTAGAGCGTATGATTTGGCGGCACTGAAATACTGGGGAGCAACGACAACAACAACAAATTTTCCA
|| || || | | || || | | | | | ||| || || | | ||| || | | ||| | | ||| |||||| |||||||||||||| || ||||| ||||| ||||| ||||| || || ||||| ||||| | | || || || ||| || |
gtatgactggaggatcttgtagcccagaactctctttataagtttccttctgagtcgtagtgaagttgaaaggacagtctgctgaacttctgagctagagcattcattggataatcaggcgacaattgcaatgtggtgaaggttgcatacgcagcatctcacgatctaa--tgtatttgggtactgtcatgtgctgagcagTATACTTAGGAGGATATGATAAAGAAGACAAGGCAGCCAGAGCCTATGACTTGGCAGCGCTCAAATATTGGGGTGT--CAGCACCACCATCAACTTCACG-
upper sequence: GLYMA10G31440.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------------------------ttagaaaaagaaataaaaac-attttttcctcatcataatat---taatatcacattattttagttgttcttcacaaataccatttcttcttgtatatttgcagGAGGTTATGATAAAGAAGAAAAAGCAGCTAGAGCGTATGATTTGGCGGCACTGAAATACTGGGGAGCAACGACAACAACAACAAATTTTCCA
|| || | | | | | | | | | | ||| | ||| || || | | ||| || | | || | | ||| |||||| ||||||||||||||||| ||||| ||||| || || ||||| || || ||||||||||| | | || || || ||| ||| |
gtatgactggagggacttgaagcacagaaccctctccatgtgcttccttctgagccgttgtgaagttcaaagaacagtctgctgaaagtttgagctagaacagtcattggatgatcaggcgatgattgctatgtggtgaaggttgtatacgcagcatctcacgatctaa--tgtgtttgggcactgtcacgtgctgcgcagTATACTTAGGAGGATATGATAAAGAAGAAAAGGCAGCCAGAGCCTACGACTTGGCAGCGCTCAAATACTGGGGTCC--CAGCACCACCATCAACTTTCCG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcacattattttagttgttcttcacaaataccatttcttcttgtatatttgcagGAGGTTATGATAAAGAAGAAAAAGCAGCTAGAGCGTATGATTTGGCGGCACTGAAATACTGGGGAGCAACGACAACAACAACAAATTTTCCA
attattttagttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagaaaaagaaataaaaacattttttcctcatcataatattaatatcacattattttagttgttcttcacaaataccatttcttcttgtatatttgcagGAGGTTATGATAAAGAAGAAAAAGCAGCTAGAGCGTATGATTTGGCGGCACTGAAATACTGGGGAGCAACGACAACAACAACAAATTTTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- agaaaaa
- - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttcac