Sequence
atgc intronic sequence ATGC exonic sequencegtacgcggttgcttgccatttcttttaatggttttaaaacaccaatgaaaaaagatttgaatagtctcacaaatttttttcagtattttcaccataaattttttaaattgagtctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
Basic information
species | Glycine max |
transcript | GLYMA19G00890.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g58130.1 (Oryza sativa), 3'ss of exon 3
-------------------gtacgcggttgcttgccatttcttttaatggttttaaaacaccaatgaa---aaaagatttgaatagtctcacaaatttttttcagtattttcaccataaattttttaaattgagtctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
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gtacgtgaatgcgaatgccttttgctgttgcatat-atacctgaccacattccttgtctatatgtgaatgcaaatgctttttactatcgcatgtatactgactacattctgtgtcctatcttatttgattagcacc----acttgatttgttttgtatgcagTTGTCCGCACGCTTACTGGACATAGGTCAAACTGCATGTCAGTTGATTTCCATCCTTTTGGAGAATTCTTTGCCTCGGGGTCACTGGACACAAATCTGAA
upper sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 3
gtacgcggttgcttgccatttcttttaatggttttaaaacaccaatgaaaaaagatttgaatagtctcacaaatttttttcagtattttcac-cataaattttttaaattgagtctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
|| |||| | |||| | | ||| | | ||| ||| || | | | ||| | ||| ||||| | | |||||| |||||||||||||| ||||| || ||||||| ||||| || |||||||||||||| || |||||||| ||||| || || ||||||||||| ||
----------------------------------------------------gtatgcaaata----tgaatatttaacttactatatatatgcatgaatcgttgag--taattctatcttttggctcgtttcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA
upper sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 4
gtacgcggttgcttgccatttcttttaatggttttaaaacaccaatgaaaaaagatttgaatagtctcacaaatttttttcagtattttcaccataaattttttaaat--tgagtctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
||| |||| | || | | | || | | | || | | || | | | | | | || | || ||| || |||||||| | ||||| |||||||| ||||||||||| | |||||||| ||||| |||||||| ||||| ||||| || || || ||||||| ||||||||
-------------------------------------------------gtaagttttgta-gttccaagagaccattcttattggactcgatttgacttctgtgagtacttacgtgttctttcacttgctttgttgagtagTTGTCAGGACTCTCACTGGTCACAGGTCCAATTGCATCTCAGTGGATTTCCACCCTTTTGGTGAGTTTTTTGCGTCAGGCTCACTAGACACAAATCTTAA
upper sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 3
gtacgcggttgcttgccatttcttttaatggttttaaaacaccaatgaaaaaagatttgaatagtctcacaaatttttttcagtattttcaccataaattttttaaattgagtctttgacttgctatgt--ttctttg-gtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
| | || | | || || | | | |||| | ||| | | | || | || | ||| ||| ||| |||| || |||| |||||||||| || |||||||| || || || ||||| | ||| |||||||||||||| ||||| ||||||||||||||||| ||| | ||||| ||||||||
------------------------------------gtatgcacattagactttgggtgtttaatat-atgaattctgttcttttgatatgttgttaaactgatatctagagattttctgttgtaatgtggttttttgtatagTTGTTCGCACGCTTACTGGCCACAGATCAAATTGCATATCTGTGGACTTCCATCCATTTGGGGAGTTCTTTGCATCTGGCTCTCTGGACACAAATCTTAA
upper sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S9_241V6.1 (Physcomitrella patens), 3'ss of exon 3
--------gtacgcggttgcttgccatttcttttaat---ggttttaaaacaccaatgaaaa----------aagatttgaatagtct-cacaaatttttttcag--tattttcaccata------aatttt--ttaaattgagtctttga-cttgct-atgtttctttg-------gtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
|| | | || || | | || | | || ||| | | ||| | | | |||| | || | ||| ||| || || || | || | || | | | | | || || ||| || | ||| | | | |||||| || |||||||| |||||| | || ||||||| |||||| || || |||||||| ||||||||||| || || || ||| |||| || ||||| ||
gtaagcttgttagagctttctctctctctcctccggtccaagtattacatgattaatttgagtttctattccatggtttgtgtggtgtgcacgtattcattctagatcatggatgcgatgcttcgtacttctaatcaggcaaaattttagatcttactgacatttttatacctgggtgcagTTGTACGCACTCTTACAGGTCATCGATCAAATTGTATATCAGTAGATTTTCATCCTTTCGGAGAGTTCTTCGCGTCGGGATCTCTAGATACAAATCTCAA
upper sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ20167 (Selaginella moellendorffii), 3'ss of exon 3
gtacgcggttgcttgccatttcttttaatggttttaaaacaccaatgaaaaaagatttgaatagtctcacaaatttttttcagtattttcaccataaattttttaaattgagtctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
||| | | | |||| | || || ||| || ||| |||| ||||| ||| ||||||| || || || || |||||| |||| || || | || || ||||| ||||| ||||||||||||||||| ||||| ||| | ||||| ||||| ||
---------------------------------------------------------------------gtaatcgtgtgaggcatttct--cgtaccgcttctaa--tgcacgtttcactt----tgtttttttt-tagTTGTCCGGACACTCACAGGTCATCGGTCTAACTGCATTTCTGTCGACTTTCATCCGTTTGGAGAGTTCTTTGCGTCTGGATCTCTCGACACCAATCTGAA
upper sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23110 (Selaginella moellendorffii), 3'ss of exon 3
gtacgcggttgcttgccatttcttttaatggttttaaaacaccaatgaaaaaagatttgaatagtctcacaaatttttttcagtattttcaccataaattttttaaattgagtctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
||| | | | |||| | || || ||| || ||| |||| ||||| ||| ||||||| || || || || |||||| |||| || || | || || ||||| ||||| ||||||||||||||||| ||||| ||| | ||||| ||||| ||
---------------------------------------------------------------------gtaatcgtgtgaggcatttct--cgtaccgcttctaa--tgcacgtttcactt----tgttttttt--tagTTGTCCGGACACTCACAGGTCATCGGTCTAACTGCATTTCTGTCGACTTTCATCCGTTTGGAGAGTTCTTTGCGTCTGGATCTCTCGACACCAATCTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcaccataaattttttaaattgagtctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
ctttgac putative branch site (score: 4)
tgtttcttt putative PPT
ataaattttttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcggttgcttgccatttcttttaatggttttaaaacaccaatgaaaaaagatttgaatagtctcacaaatttttttcagtattttcaccataaattttttaaattgagtctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA