Sequence
atgc intronic sequence ATGC exonic sequence...ttttgatgataataaaattaatttaaaactctttctcttcctttgctaaacatttcccactttttacattttcattgctgcttatttttttctggtgcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
Basic information
species | Glycine max |
transcript | GLYMA19G41840.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
------ttttgatgataataaaattaatttaaaactctttctcttcctttgctaaacatttcccactttttacattttcattgctgcttatttttttctggtgcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
| ||| | ||| | || | | | ||| | | | | || | | | | || | | || | ||| | || | ||||| ||| |||| || ||||| |||||||||||||||||||| ||||| || || || ||||| || ||||| || || |||| ||||| |||| ||
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattcc-ctacttcacattgtgtt-----gtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G116506_T01 (Zea mays), 3'ss of exon 1
ttttgatgataataaaattaatttaaaactctttctcttcctttgctaaacatttcccactttttacattttcattgctgcttattttt--ttctggtgcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
||||| | | | ||| | | | || | || | || | || | | | | | | || || || || || ||| | ||| |||| || ||||| ||||||||||||||||||||||| | || | || ||||| || ||||| || || ||||| ||||| |||| ||
-actgatgttctcccacgttcttttatcccagaaatggaactat-ctgtgcgttgatattctactataatgtagtaattccctacttcacattgtgttgtagGTTTGAGCAAGAGTCGGGGTTCTTCTTCAATATGAAGTACTTTGAAGCGAAGGGCCATGCTGGGGACTGGGATGAGGTGGAGAAATACTTGTCAGGTTTC
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 1
ttttgatgataataaaattaatttaaaactctttctcttcctttgctaaacatttcccactttttacattttcattgctgcttatttttttctggt--gcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
|||| | | | || || || | | | | | | | | | | ||| | | ||||||||| || | | ||||| |||||||| || |||||||||||||||||||||||||||||||| ||||||||||| || |||||||| |||||||||||||| ||| | || | |
tttttttttttttcttctt--ttccaatttacactttcttggaagtttggtgtagttaattaatcttaatttgaacggaaattattttttggtgttttgtagGCTTGAGAAAGAGTCAGGGTTTTTCTTCAATATGAAGTACTTTGAGGAGAAAGTACAGGCAGGAGAATGGGATGAAGTTGAGAAGTATTTATCCGGATAT
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 1
ttttgatgata-ataaaattaatttaaaactctttctcttcctttgctaaacatttcccactttttacattttcattg-ctgcttattt----ttttctggtgcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
| | || | || | | | | || | | | | | || ||| ||| | || | | || ||| || | | |||| |||| | ||| ||||||| || || ||||||||||||||||||||||| || |||| || | |||||| ||||| || || || || ||| | |||||
--tctgcgttacgtgaagctggtgtcattttcaaaatgtgcata---cagacgtttgtttcttctgcaatctgtactgactggttttataataccttctaac-cagGTTGGAGCAAGAATCAGGATTCTTCTTCAATATGAAGTACTTTGAAGACCAAGTTCAAGGTGGTGAGTGGGAGGAGGTGGAACGATATTTATCTGGGTTC
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 1
ttttgatgataataaaattaatttaaaactctttctcttcctttgctaaacatttcccactttttacattttcattgctgcttatttttttctggt----gcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
| | | || ||| | | | || | | || | | | || | || | ||||||| ||| |||||||||| || | |||||| |||||||||||||| || | || ||| ||| || ||||| || || |||| |||||| | || ||
--------------------------------------------gtgagaagatttgtggtttgttcttgttggtggatg-taagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
upper sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 1
ttttgatgataataaaattaatttaaaactctttctcttcctttgctaaacatttcccactttttacattttcattgctgcttatttttttctggt---gcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
| | | || ||| | | | || | | || | || | | | ||||||| ||| |||||||||| || | |||||| |||||||||||||| || | || ||| ||| || ||||| || || |||| |||||| | || ||
--------------------------------------------gtgagaagatttgtggtttgttcttgttggtggatgtaagtgttgtgcgattttggcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaaacatttcccactttttacattttcattgctgcttatttttttctggtgcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
tgctaaa putative branch site (score: 2)
ctgcttatttttttct putative PPT
tttttacattttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgatgataataaaattaatttaaaactctttctcttcctttgctaaacatttcccactttttacattttcattgctgcttatttttttctggtgcagGCTCGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT