Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA19G41840.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG
|| | | | ||||| | |||| | || || ||| || | | | | || | || |||| || ||| | || |||| || || ||||| |||||||||||||| |||| | | ||||| ||||||||||||||| || |||| ||||| ||||| |||||| | ||
---------------gtaagcagaggtatt--actttcgtaccgaa----------agttgtctttagttat----tgttgttgtactaatttacttgtttttcata-----tgaagGTTGTTCTCATGTGGAACAAGTAAAGATGGAGATTCATATTTAGTTGAGTGGAATGAAAGTGAAGGATCTATCAAGAGGACATATTCTGGGTTTCGTAAA
upper sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------------------------------------------gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatgg-ataattaagatgt--attaaataaaaccgtattaacatgtcttcctatttgtcttccattattt-------ctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTT-CAGAAAG
| || || | | | | || | | || | | | | | || || | || || | || |||| | | | | || ||| | ||| || ||| |||| ||||| ||||| |||||||||||||| || || || ||||| ||||||||||||||| || | ||||| || || || || | ||| ||||||
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggagg-atactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttctgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA-
upper sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
--------------------------------------------------------------------------------gtaagaaggatttgggtgcggataagtatttaagtttca-tgttcaatggataattaagatgtattaaataaaaccgtattaac--atgtcttcctatttgtcttccattatttctat-agACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG
| || | | | | | | || | | ||| | | | || || || ||| | | ||| | |||| || | | || ||| | | | || || | | ||| |||| ||||| ||||| ||||||||||| || || ||| | ||||||||||||||||||||| |||| || ||||| || || |||||||| ||||||
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaa-atatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG
upper sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG
| | | | | | ||| || || || | | | ||||| |||| | | ||| || ||| |||| | || | ||| || || ||||||||||| |||||||||||||| || | ||| || ||||||||||| ||||| | || || ||| | |||||| || ||| | |||
-------------aatgatgatttactgtcagaatttgatcctccatctttttcttacatgtagaggtatcgtgaatattgatttatctccccttttctctttt-tgatgt---tagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG
upper sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 14
gtaagaaggatttgggtgcggataag--tatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG
| | | || || | | | | ||| ||| | | |||||| | || | || || | |||| | | | | | |||| |||||||| |||||||| |||||||||||||| | ||| || ||||||||||| || ||| | || |||||| | |||||| || ||| | |||
-----------tcgctttcgaattaagttgagtgaatttaggacgtgatg--tgtccatcttgtatttgcgacaatgatttt----tgattatgaattttttctttgtggacgcca--gACTCTTTTCTTGTGGAACTAGCAAAGATGGAGAATCTTATCTGGTGGAATGGAATGAGAGCGAAGGCGCAATTAAGCGGACATACTCAGGTTTCCGCAAG
upper sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacat---gtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG
| | ||| | || || | || | ||| || ||| | ||| |||||||||| ||||| || || ||||| || || |||||||| || ||||||||||||||| | || ||||| | || |||||||| || | ||
-----------------------------------------------------------------------gtttgcttcaacctttggtatttccatca--catcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
upper sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 14
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG
| | ||| | | | | | || || | ||| |||||||||| ||||| || || ||||| || || |||||||| || ||||||||||||||| | || || || | || |||||||| || | ||
-----------------------------------------------------------------------gtttgcttcaacctttggtatttccatcacatcctttgttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATAAAAAACACCTACAATGGTTTTCGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG
tattaac putative branch site (score: 1)
tcttcctatttgtctt putative PPT
attatttctata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA