Sequence
atgc intronic sequence ATGC exonic sequence...ttatgtcttatgtgggatatattagatttttatgggtaatacataatcatatactgtagtacttgtgctttccttcaataatttttttctttcttgctagGTTATGGCATTGATTGCTTACTTGATGGAATTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTTTG
Basic information
species | Glycine max |
transcript | GLYMA16G03950.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G03950.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g02290.1 (Oryza sativa), 3'ss of exon 6
---------------------------------ttatgtcttatgtgggatatattagatttttatgggtaatacataatcatatactgtag---tacttgtgctttccttcaataatttttttctttcttgctagGTTATGGCATTGATTGCTTACTTGATGGAATTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTTTG------------
| | || | |||| || || |||| | | | ||| | || | | | || || || || | | | ||||||||| | ||||||| |||||||||||||||||||| || ||||| |||||||| ||||| || || |||||||| |||
gtgtggatttcttattccgttctacctgctagacttttgctatttcacaatattttcttttattatctcatttgcctccccatttccttttgccctgctagtaacatctttttgtggccaccaattgaataaatagGTTATGTCTCTGATTGCATACTTGATGGAATTTAAAGGGAATTATGGACCACATCTCATAATTGTACCGAATGCTGTCTTGGTCAACTGGAAG
upper sequence: GLYMA16G03950.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 6
---------------------------------ttatgtcttatgtgggatatattagatttttatgggtaatacataatcatatactgt--agtacttgtgctttccttcaataatttttttctttcttgc--tagGTTATGGCATTGATTGCTTACTTGATGGAATTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTTTG------------
| |||| ||||| || ||| | | | | | | | || | | | | || || || | | | ||| ||| ||||| ||||||||| |||| ||| |||||||||||||||| || |||||||| ||||| |||||||| ||||||||||| ||
gtcattccttgcttattcttgtttactttctgtactcctgttattcatgatattttttattatcgtcaatgcttcctcttttcattcgaccaatggccaggaacttatttgtatgtctatgctatttgttgtaatagGTCATGGCATTGGTTGCGTACCTGATGGAATTTAAAGGGAATTATGGCCCTCATCTCATAATAGTGCCAAATGCTGTCTTAGTCAATTGGAAG
upper sequence: GLYMA16G03950.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0046g02290.t01 (Vitis vinifera), 3'ss of exon 6
--------ttatgtcttatgtgggatatattagatttttatgggtaatacataatcatatactgtagtacttgtgctttccttcaataatttttttctttcttgctagGTTATGGCATTGATTGCTTACTTGATGGAATTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTTTG------------
| | || | | ||| | | | | | | || | | | | | || |||||| | | | ||| ||| || | | |||| |||||||| |||||||| |||||||| || |||||||||||||| ||||||||||| || || || ||||||||| ||
gtgaatttctgcatattccttatggcatactgcaactactttcaaattttatgttta-acaattaagggtttgtgcagtgtt----tgattgtttctttattggacagGTAATGGCATTAATTGCTTATTTGATGGAGTTCAAAGGAAACTATGGTCCACATCTTATTATTGTTCCTAATGCTGTTCTGGTAAACTGGAAG
upper sequence: GLYMA16G03950.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ33371 (Selaginella moellendorffii), 3'ss of exon 2
ttatgtcttatgtgggatatattagatttttatgggtaatacataatcatatactgtagtacttgtgctttccttcaataatttttttctttcttgctagGTTATGGCATTGATTGCTTACTTGATGGAATTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTTTG------------
|| | || | | | |||| || || ||| | | |||||||||| | ||||| ||||||||||| || |||||||| || || ||||||||||| || || || || || || |
-----------------------------------------gttagctttgtattttgaggtccgggcttgtctgagatgttttcgtcc---------agGTTATGGCGCTCATTGCATACTTGATGGAGTTCAAAGGAAATTACGGACCACATCTTATTATTGTTCCCAACGCAGTCATAGTGAACTGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcatatactgtagtacttgtgctttccttcaataatttttttctttcttgctagGTTATGGCATTGATTGCTTACTTGATGGAATTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTTTG
ctttccttcaataatt CT-rich tract
ttcaataatttttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatgtcttatgtgggatatattagatttttatgggtaatacataatcatatactgtagtacttgtgctttccttcaataatttttttctttcttgctagGTTATGGCATTGATTGCTTACTTGATGGAATTTAAAGGAAACTATGGCCCACATCTTATAATAGTCCCAAATGCTGTTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - tgtggga
- - - - - - - - - - - - - - - - - - - - - - - -catatac