Sequence
atgc intronic sequence ATGC exonic sequence...ctattagaatctattgttcagacacacattttttggttcaaattaggtaaactagtttttgttttcatggttgtttttgtgactctatttttgagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
Basic information
species | Glycine max |
transcript | GLYMA13G00420.1 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 8
---------------------ctattagaatctattgttcagacacacat--------tttttggttcaaattaggtaaactagtt-------tttgttttcatggttgtttttgtgactctattttt--gagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| || | | | | || | |||| | ||| ||| || | | || | || | ||| | ||||| |||| | | ||||||| || ||||||||||| |||||||||||||| |||||||| |||||||| ||||| ||||| |||||| ||||||||||||||||||||||||| |||
gtacatacataattgggaattttgttttgaacaaataaaaggataaacataatggttttatttcaatcagatgaagacaatcgatcatgcatgttgatgcacatttctaattttgatctcttattcctcctaatttagGCAGACATTGGTCTTGCTATGGGTATCCAAGGAACAGAAGTAGCTAAAGAAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
ctattagaatctattgttcagacacacatt---ttttggttcaaattaggtaaact--agtttttgttttcatggtt--gtttttgtgactctatttttgagtt--tagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| ||| || ||| | || | || || || | || || | || ||| | || ||| | | | || | | || ||||| ||||| ||||| | ||||| ||||| || || |||||||| || ||||| |||||||| || || ||||||||||||||||| || || |||| |
--------gtttatctctc-gactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------ctattagaatctattgttcagacacac-attttttggttcaaa---ttaggtaaactagtttttgttttcatggttgtttttgtgactctatttttgagt-ttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| | | || | | | || ||| |||| | | || | | | ||| || | | | | || | | | ||| | | |||| |||||||||||| | ||||| |||||||| |||||||| || ||||||||||| || || || ||| |||||||||||||| |||| |||||||||
gtacattcaatttgggagttcatattttaaatgaatacaagaattcaacatgcatgtgattatatgaagcactatttggtaatacagcacttctaacatgttgaggtttcttccccttctcaatcttatcatt--attcccacttatcagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
-----------------------------------ctattaga--atctattgttcagacacacattttttggttcaaattaggtaaactagtt---tttgttttcatggttgtttttgtgactctattt--------ttgag-------------tttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
|| | | | | | || |||| | ||| | |||| | || |||| || | ||| ||| | |||| | || ||| ||||| | |||| ||||||||||| ||||||| || || || || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| || || |||| |
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G138195_T01 (Zea mays), 3'ss of exon 1
----------------------------------ctattagaatc--tattg-ttcagacacacattttttggttcaaattaggtaaactagtt---tttgttttcatggttgtt------------tttgtgactct-------atttttgagttt--agGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
|| || | || | || |||| | ||| | |||| | || |||| || | ||| ||| | |||| ||||| | | | | | | || || | ||||||||||| ||||||| || || || || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| || || |||| |
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcatcggtttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtactcgacaaactctgaaacttgcagACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
-----------------------------------------ctattaga--atctattgttcagacacacattttttggttcaaattaggtaaactagtt---tttgttttcatggttgttt-------------------ttgtgactctatttttgagttt--agGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
|||| | | | | || | ||| | || |||| | || |||| || | ||| || | |||| | || | | | | | | || |||| ||||||||||| ||||||| || || || || |||||||| || ||||| |||||||| ||||| |||||||||||||| || ||||| |||| |
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 26
-----------------------------------------------ctattagaatctattgttcagacacacatttt---ttggttcaaattaggtaaactagtttttgttttcatggttgt---ttttgtgactctatttttgagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
||| ||| | | || | || ||||| | ||| | | | | | | || | | |||| | |||| ||| | ||||| |||| |||||||||||||| ||||| || ||| |||||||| ||||| ||||| || || ||||| || ||||||||||| |||||||||||||| |||
gtatagtaatttactgaaatttaaactgataatgtcgaaagctacatctaactgaaagtttcttttggccaagtattttgcctacgtttttactcagcgagcggatcattatctcattggtgttaaattttttgagtgtatttgc------agGCAGATATTGGTCTTGCTATGGGAATAGCAGGAACAGAAGTGGCTAAGGAGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
ctattagaatctattgttcagacacacattttttggttcaaattaggtaaactagtttttgttttcatggttgtttttgtgactctatttttgagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| ||| ||| | | || | | | | || | || ||| | || ||| || | | ||| | | | || |||| ||||| ||||| ||||||||||||||||| || |||||||| || || | || || |||||||| ||||||||||| |||| || |||||||||
---gttcaatacatttacattcctcgtatgtgtaagctttaa--aaatacactgttattgaggatcacactt-tctgtgttgccccccaact---ttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
----------ctattagaatctattgttcagacacacattttttggttcaaattaggtaaactagtttttgttttcatggttgtttttgtgactctatttttgagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| || |||| || | | | | ||||||||| | | | | | ||||| | | || ||||| | | | |||| || ||||||| |||||||||||||||||||| || ||| ||||| ||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||| |||
ctcaaataggtttctaatatcttttatataaaaa-acatttttttatat--------tttccccgctcttgttcgcctt-ttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtaaactagtttttgttttcatggttgtttttgtgactctatttttgagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
ctctattttt CT-rich tract
tatttttgagttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctattagaatctattgttcagacacacattttttggttcaaattaggtaaactagtttttgttttcatggttgtttttgtgactctatttttgagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgtt