Sequence
atgc intronic sequence ATGC exonic sequence...tgtgcttgcttcattggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
Basic information
species | Glycine max |
transcript | GLYMA08G42170.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 4
--------------tgtgcttgcttcattggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactat--gactggtg-gcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
| | ||| | |||| | | || | || | | || | | | ||| | || | | | | |||| |||||| ||||| ||||||||||||||||| || ||||| || ||||||||||| || |||||||||||| | || ||| || ||||||| || |||||
gtaagaaacaaaccatcgtccccgtcaaaaagaaaagaattgttcttcactttagctcttttat-atgtatatgtttagttgcataacccattttccataactgaattggtatacagGCTTGCTTATTTACATGAAGCAATAGAGCCAAAAGTTGTACACCGGGATATCAAATCAAGCAACATACTAATCGATGAAGAATTCAATGGCAAACTTTCT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G017386_T03 (Zea mays), 3'ss of exon 4
tgtgcttgcttca--ttggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
| | |||| | || ||| |||| || | | || || || | || || | || | | ||||| |||| ||||||| |||||| | |||||||| || || || ||||| || || || |||||||| ||||||||||||||||||||| ||| || |||| || || |||
---gtaagtttcaatcttaatctgtaagttacctacatagtttcctgtgtttttagctgtataaaattggttcttattttt-ctaattatga-tggttgcagGCTTGCTTACCTTCATGAAGCTATTGAGCCAAAAGTTGTACATCGAGATATAAAATCAAGCAACATATTGATTGATGATGAATTTAATGGCAAAGTATCT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 2
tgtgcttgcttcattggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttacta-tgactggtg-gcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
| | || ||| ||| || || || || || | || || || | | | | | || || | ||| | ||| | |||||| ||||| ||||||||||| |||||||| ||||| || ||||| ||||| || || ||||| || || |||||| || ||||||| ||| |||||
-------gtaagaaatgaaacc--attcacaattttg-catcttttatat---gcatacatttattaaattaagatgttgtctacaactgaacactatacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTACACCGTGATATCAAATCGAGCAATATCTTAATTGATGAAGAATTCAATGGCAAGCTTTCT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 4
tgtgcttgcttcattggatacctaatttactgttatggcagtttcaacattaggccta-attccactgattaaactccttatttact--atgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
| || ||| | | || || | || || || || || | ||| || | || | |||| |||||| ||||| ||||||||||| |||||||| ||||| || ||||| ||||| || || ||||| || | ||||| || ||||||| ||| |||||
----------gtaagacatggaccattcaatattttgtctcttctttgat---gcatatgttttgccatctaaggcatttttataattgatgatatactacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTGCACCGTGATATCAAATCTAGCAATATCCTAGTTGATGAAGAATTCAATGGCAAGCTTTCT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
tgtgcttgcttcattggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
|| || || | | | | | |||| | | ||||| || | ||| | | | | || | || || ||| | |||||| |||||||| ||||||||||||||||| ||||| || ||| | || ||||| |||| || |||||||||||| ||| || |||||||| | |||
-gtaagtggtttg--aaacagtttagcttttgttg-gatatgttcaat-----gcttgatt--attaaa-agggtctgcaatttgtacaact--ttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
-tgtgcttgcttcattggatacctaattta--ctgtta-tggcagtttcaacattaggcctaattccactgat-taaactccttatttactatgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
| | | | | || | || || ||| | | | |||||| | | || || ||| | || | | ||||| | | | |||||| ||||| |||||||||||||||||||| ||||| || ||| | || ||||| ||||||| || ||||||| ||| |||||||||||| |||||
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactct--ttaaggggatattgacatgctctgtactacaatt--ttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
upper sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 5
tgtgcttgcttcattggatacctaatttactgttatggc--agtttcaacattaggcctaattccactgattaaactcctta----tttactatgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
| | |||| || || | | | | || ||||| | | |||| ||| | | | | || ||| ||||||| || || || ||||| ||||||||||||||||| ||||| || || ||||| ||||||||||| ||||||||| ||| ||||||||||||||||||
------tattccattcagaactgaaatctactccagaactgaaattgaacatcttggtctttcacactttgaaaaagtcaaaaaaatgtttcatattgggttgcagGCTTGCCTATTTGCATGAGGCAATAGAACCGAAAGTTGTTCATCGAGACATAAAATCAAGCAACATCTTGATTGATGATGAGTTCAATGCAAAGGTTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacattaggcctaattccactgattaaactccttatttactatgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
cactgat putative branch site (score: 3)
ttatttactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgcttgcttcattggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG