Sequence
atgc intronic sequence ATGC exonic sequence...tctattagaatctattgttctgacacattttttggttcaaattatgtgaactagtttttgttttcatggttgtgtttgtgactctatttttggagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
Basic information
species | Glycine max |
transcript | GLYMA17G06520.1 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 8
------------------------------tctattagaatctattgttctgacacattt-tttggttcaaattatgtgaactagtttt---tgtt--ttcatggttgtgtttgtga---ctctatttttggagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| | || || || | | ||| ||| ||| || | | || | | |||| | || || | || ||| || | | | ||||||| || ||||||||||| |||||||||||||| |||||||| |||||||| ||||| ||||| |||||| ||||||||||||||||||||||||| |||
gtacatacataattgggaattttgttttgaacaaataaaagg-ataaacataatggttttatttcaatcagatgaagacaatcgatcatgcatgttgatgcacatttctaattttgatctcttattcctcctaatttagGCAGACATTGGTCTTGCTATGGGTATCCAAGGAACAGAAGTAGCTAAAGAAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAG
upper sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
-tctat-tagaatctattgttctgacacattttttggttcaaattatgtgaactagtttttgttttcatggttgtgtttgtgac-tctatttttggagtt--tagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| ||| | ||| ||||| || |||| | ||| || | | || ||| | || | | | | | || | || ||||| ||||| ||||| | ||||| ||||| || || |||||||| || ||||| |||||||| || || ||||||||||||||||| || || |||| |
gtttatctctcgactaatgttccatcatgtttt--gaaagaaacaatct---tcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
upper sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------tctattagaatctattgttctgacacattttttggt--tcaaattatgtgaactagtttttgttt--tcatggttgtgtttgtgactctatttttggagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
|| | | || | | | ||| || | |||||| | | | ||| ||| |||| || | | | | |||| | |||| |||||||||||| | ||||| |||||||| |||||||| || ||||||||||| || || || ||| |||||||||||||| |||| |||||||||
gtacattcaatttgggagttcatattttaaatgaatacaagaattcaacatgcatgtgattatatgaagcactatttggtaatacagcacttctaacatgttgaggtttcttccccttctcaatcttatcattattcccacttatcagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAG
upper sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
--------------------------------tctattagaatcta---ttgttctg---acacattttttggttcaaattatgtgaactagtt---tttgttttcatggttgtgtttgtgac-tctatttttggagttt-------------------agGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| || ||| | | | ||| || | | ||| | |||| | ||||| | || | ||| ||| | ||| | || ||| || || | || |||| ||||||||||| ||||||| || || || || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| || || |||| |
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
upper sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM2G138195_T01 (Zea mays), 3'ss of exon 1
---------------------------------tctattagaatc--tattgttctg---acacattttttggttcaaattatgtgaactagtt---tttgttttcatggttgtg------------tttgtgact------ctatttttggagttt--agGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| || || | || | | || | | ||| | |||| | ||||| | || | ||| ||| | ||| ||||| | | | | | || | || || | ||||||||||| ||||||| || || || || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| || || |||| |
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcatcggtttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtactcgacaaactctgaaacttgcagACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG
upper sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
---------------------------------------------------------------tctattagaatctattgttctgacacattttttggttcaaattatgtgaactagtttttgtttt-catggtt--gtgtttgtgactctatttttggagtt-tagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
|| | || | | || | | | ||| | | | | || | || ||| || || | || | | | | | | || |||| ||||||||||| ||||||| || || || || |||||||| || ||||| |||||||| ||||| |||||||||||||| || ||||| |||| |
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
upper sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 26
------------------------------tctattagaatctattgtt--ctgacacattttttggttcaaattatgtgaactagtttttgttt----------tcatggttgtgtttgtgactctatttttggagttta------gGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| | || ||| | |||| | || ||| | ||| | | || |||||| | |||| | || ||| | |||||| |||| || ||| |||||||||||||| ||||| || ||| |||||||| ||||| ||||| || || ||||| || ||||||||||| |||||||||||||| |||
gtatagtaatttactgaaatttaaactgataatgtcgaaagctacatctaactgaaagtttcttttggccaagtattttgcctacgtttttactcagcgagcggatcattatctcattggtg-ttaaattttttgagtgtatttgcagGCAGATATTGGTCTTGCTATGGGAATAGCAGGAACAGAAGTGGCTAAGGAGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAG
upper sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
tctattagaatctattgttctgacacattttttg-gttcaaattatgtgaactagtttttgttttcatggttgtgtttgtgactctatttttggagttt-agGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| | | | ||| | | || || | | || | || || | | | || | | ||| |||| ||||| ||||| ||||||||||||||||| || |||||||| || || | || || |||||||| ||||||||||| |||| || |||||||||
---------gttcaatacatttacattcctcgtatgtgtaagctttaaaaatacactgttatt--gaggatcacactttctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG
upper sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
---------tctattagaatctattgttctgacacattttttggttcaaattatgtgaactagtttttgttttcatggttgtgtttgtgactctatttttggagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
| || |||| || | | | | | |||| || | ||| | | | | ||||| | | || | ||| | | |||||||| ||||||| |||||||||||||||||||| || ||| ||||| ||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||| |||
ctcaaataggtttctaatatcttttata-taaaaaacatttt--tttatatttt----ccccgctcttgttcgcct--tttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaactagtttttgttttcatggttgtgtttgtgactctatttttggagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
ctctattttt CT-rich tract
tttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctattagaatctattgttctgacacattttttggttcaaattatgtgaactagtttttgttttcatggttgtgtttgtgactctatttttggagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - -ctgacac
- - - - - - - - - - - - - - - - - - - - - - tgtgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgtg