Sequence
atgc intronic sequence ATGC exonic sequence...tatttatgctttatacattgttcagataaattattagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
Basic information
species | Glycine max |
transcript | GLYMA17G08830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
--tatttatgctttatacattgttcagataaattattagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatata--tttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
|| ||| ||| | | | || | | | | | ||||| | |||| ||| |||| ||||| ||| | | || |||||||| |||||||| ||||||||||| || ||||| || ||||||||||| || | |||||||| ||||||||||| || ||||| | ||| | || ||
atcatagtggctccatatagaagttaaatttgtcaaaatctt--ataccataaagttcatttttgttttttgttt--cttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
tatttatgctttat-acattgttcagataaatt--attagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctg-catatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
|| || | | | ||| || || || |||| | || | | | || || ||| | ||||| | | | | | |||||||| |||||||| ||||||||||| || ||||| || ||||||||||| ||||| || ||||| |||||||| || || || || | ||| | || ||
----taagcatcgtgatggcgttatgagaagttaaattatgttttaagtcttataccagaaatttctctttattgattcttaacaagataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA
upper sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
tatttatgctttatacattgttcagataaatt--attagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
|| | | | | || || || || || | | || | |||| || || ||||| ||| || | |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | |||||||| ||||||||||| || ||||| | ||| | || ||
--ttctaatcacagatagtcttaggaaaatttccatacaagttgcagtttcgtctatattttatagcactgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
tatttatgctttatacattgttcagataaatt--attagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatattt--ttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
|| | | | | | || |||| || | | ||| | |||| || | ||||| | || || | |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | |||||||| ||||| ||||| || ||||| | ||| | || ||
---cta-atcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA
upper sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
tatttatgctttatacattgttcagataaatt--attagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttt--tggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
|| | | | | | || |||| || | | ||| | |||| || | ||||| | || ||| |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| ||| | |||||||| |||||
---cta-atcgcagatagtcctaggaagaattccatacaagttgcacttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
upper sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G009154_T01 (Zea mays), 3'ss of exon 2
tatttatgctttatacattgttcagataaatt--attagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
|| | | | | || || || || || | | ||| | |||| || ||| |||| ||| || | |||||||| |||||||| |||||||||||||| ||||| || ||||||||||| | | |||||||| ||||||||||| || ||||| | ||| | || ||
--ttctaatcacagatagtcttaggaaaatttccatacaagttgcagttttgtctatattttatagcattgagagttcttatcagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCTGTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
tatttatgctttatacattgttcagataaattattagtatgaaaaccatgttttagttt--ttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
| ||| || |||| | || | | || | ||| ||| | | | | |||| | | ||| | | | | | ||||||| |||||||| || |||||||| || || ||| | |||||||| || |||||||||||||| ||||| ||||| || |||||||| ||| ||||
-----gtaagttactca--gttcttgaactctaccaaaacaaatttgacttttgagtgaaatgaaaactgagttttggcttttctttttctgctgt-gacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
upper sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 3
tatttatgctttatacattgttca--gataaattattagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
| || | |||||| | ||||| || | | | | ||| | || ||| || || |||||| | | | | |||||||||| ||||||||||| ||||| ||||| |||||||||||||||||||| || || || ||||| || | ||||| |||||||| || || |||||
-aggatggcaagacacattgacaatggataatttgtgttcttaatatgcatttaaagagttctcaagatttaactaatctaatcttcctgt-cctatggcagTGACTTGGAATGTTACTTGCACGTATTCACAATTCCTGGCTCAGAAGACGCCTACATGTTGTGTCTCATTGTCATCGTTCTATAATAACACTATAGTATC
upper sequence: GLYMA17G08830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
---tatttatgctttata-cattgttcagataaattattagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
| | || ||| | || | || | | || | ||| | | | | | || | | || || | | | | | || ||||||| ||||||||||| ||||| ||||| ||||||||| ||||||| ||||| ||||||||||| || |||||||| ||||| || | ||| | |||
agggagtgattcttaaaggcaatttttgtct---tccctaattaaaaatttgagctattacccat-aaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatgttttagtttttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
gcttaat putative branch site (score: 4)
tattttt putative PPT
atatattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttatgctttatacattgttcagataaattattagtatgaaaaccatgttttagtttttcagatttggtttagcttaatctgcatatatttttggcagTGACCTGGAATGTTACCTGCACATATTCTCAATTCCTGGCTCAGAAGACCCCAACTTGCTGTGTTTCTCTCTCATCCTTCTATAACAATACAGTAGTAAA
- tttatgc
- - - - - - - - - - - - - - - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatat