Sequence
atgc intronic sequence ATGC exonic sequence...tgtttgtacgtttcaaaatttagaacatgtgttctatgctaggatgcacttgatacatgatttggttggttaagtctaatgtctgttctgacatttgaagGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
Basic information
species | Glycine max |
transcript | GLYMA16G17830.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g48990.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------tgtttgtacgtttcaaaattta-gaacatgtgttctatgctaggatgcacttgatacatgatttg-gttggttaagtctaatgtctgttctgacatttgaagGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
| || || | || | || ||||| || | | | || || |||| || | || || ||||| ||| |||| || ||||||||||||||| | ||||| || || ||| ||||| |||| || || || |||||||| |||||||||||||| ||||| || || || || |||||
gtaaagacactgtctattctttgagttgatctgaaaactgtactacactttgatgcatttttactaggactctatggatatgaacaattgcttcccac-ataatttctttactacaacatgtatactgattgcatctaac-tcttctctg----ttaaagGATTTTGAATTTCATGAGCTAGAGGAGGTGCTGCAGTATTATCCCCATGGTTATCATGGTGTTGACAAGGAAGGAAGGCCCGTCTATATCGAGTTGCTTG
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G014994_T03 (Zea mays), 3'ss of exon 3
-----------------------------tgtttgtacgtttcaaaatttagaacatgtgttc-----tatgctaggatgcacttgatacatgatttggttg------gttaagtctaatgtctgtt-ctgacat------ttgaagGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
| | | || ||| | | || | || || | || ||| | | | ||| || | || | | || | | || || || | |||||||||||||||||| | ||||| || || || ||||| |||||||||| || || ||||| |||||||||||||| ||||| || |||||||| |||||
gtaggatgttgtctattctaaaaagttgatctcaaaatcttatgaaactctgctgatatattgacgtatacgataagat-tattcatcatatgcttctgcaaaactatgtcatgcatactaacagtagctaacttcactcattgaagGATTTTGAATTTCATGAGCTAGAGGAGGTCCTGCAGTATTACCCTCATGGTTACCATGGGGTTGACAAGGAAGGAAGGCCTGTGTACATTGAGTTGCTTG
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G459982_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------tgtttgtacgtttcaaaatttaga-acatgtgttctatg----ctaggatgcacttgatacatgatttgg------ttggttaagtctaat-------gtctgttctgacatttgaagGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
| || | | | || || ||||| |||||| ||| ||| | | ||||||| | | | | | || | | | | | |||||||||||||||||| | || || || || || |||| |||| ||||| || || ||||| |||||||||||||| ||||| || |||||||| |||||
gtaggatgttgtctactctagaaagttgatctcaaagttatatgaaactctgctgatatatagatgtatttacatgcactctatggcttctaagat-tgttcatcatatgattttgcaaaactatgccatgccttttaacagtagcttactgtactcgttgaagGATTTTGAATTTCATGAACTAGAGGAGGTCCTGCAATATTATCCTCATGGTTACCATGGGGTTGACAAGGAAGGAAGGCCTGTCTACATTGAGTTGCTTG
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G452580_T03 (Zea mays), 3'ss of exon 4
--------------------------------------------------------tgtttgtacgtttcaaaatttagaacatgtgttctatgctaggatg-cacttgat---acatgatttggttggttaagtctaatgt---ctgttctgacatttgaagGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
| | | | || | | || | ||| ||||| | | | || |||| || | | || | | | || | | | |||||||||||||||||| | || || || || || |||| |||| ||||| || || ||||| |||||||||||||| ||||| || |||||||| |||||
gtaggatgttgtctactctaaaaagttgatctcaaagttatatgaaactctgctgatatatagatgtatttacatgcactctatggcttctaagattgttcatcatatgattctgcaaaactatgtcatgcatattaacagtagcttactgtactcgttgaagGATTTTGAATTTCATGAACTAGAGGAGGTCCTGCAATATTATCCTCATGGTTACCATGGGGTTGACAAGGAAGGAAGGCCTGTCTACATTGAGTTGCTTG
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------------tgtttgta-cgt-ttcaaaatttaga-acatgtgttctatgctaggatgcacttgatacatgatttggttggttaagtctaatgtctgttctg-acatttgaa-----gGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
||| | | | | | |||| || || | | || | || | || | ||| | | ||| ||| || | | || || |||| ||||||||| || |||||||| |||||||| ||||| | || |||||||| |||||||||||||| |||||||| || || || ||||||||||| ||||
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctgga-ttagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 4
---tgtttgtacgtttcaaaatttagaacatgtgttctatgctaggatgcacttgatacatga---tttggttggttaagtctaatgtctgttctgac-atttgaagGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
|| | | ||| | || || || | |||| ||| ||| | ||| || ||| ||| |||| |||| | | ||||||| |||||||| |||||||||| || || || || | ||||||||||| || ||||||||||| |||||||| ||||||||||||||||| || ||||
tactgctcttggcttt-----tctacaatggatgatttatga-gaaatgtttttgttttctgaacattatattgcctaatcctaaca-ctgtataatcgaaatgaagGACTTTGAATTCAAAGAGCTGGAGGATGTCTTACAATACTACCCTCAAGGATACCATGGAGTTGATAAGGAAGGAAGGCCAGTTTACATTGAGAGACTTG
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
tgtttgtacgtttcaaaatttagaacatg-tgttctatgctaggatgcacttgatacatgatttggttggttaagtctaat--gtctgttctga--catttga--agGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
| | ||| | | || |||| || | |||| ||| ||| | | | || | | ||| || | ||| ||| | || | |||| || ||||| ||| | || ||||| | | | || ||||||||||||||||| || || || ||||| ||||| || ||||||||||| |||
----tacgtgcttcgacacc-agtacatactgatttatgtgagggggcatatattgtctctttatatca--cgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcacttgatacatgatttggttggttaagtctaatgtctgttctgacatttgaagGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
ttctgac putative branch site (score: 2)
atgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttgtacgtttcaaaatttagaacatgtgttctatgctaggatgcacttgatacatgatttggttggttaagtctaatgtctgttctgacatttgaagGATTTTGAATTTGAAGAGCTGGAAGAAGTGTTGCAGCATTACCCTCAAGGGTATCATGGAGTTGACAAGGAAGGTAGGCCAGTTTACATTGAAAGGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
tgtttgt
- - - - - - - - - - - - acatgtg
- - - - - - - - - - - - - - - - -ctatgct
- - - - - - - - - - - - - - - - - - - - -ggatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - -tacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttgg