Sequence
atgc intronic sequence ATGC exonic sequence...cttgtttatcttggttttagcttgatgattactggcacactgtcatgggcaatctaattagtaattattacaatctaattaactgtttttgtgatgacagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA
Basic information
species | Glycine max |
transcript | GLYMA17G24130.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 6
------------------------cttgtttatcttggttttagcttgatgattactggcacactgtcatgggcaatctaattagtaattattacaatctaattaactgtttttgtgatgacagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA---
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gtgtttaacctatagaccctatctttcatttattttggtttagtcttgcctcgtttttgtcctacatgttttactatttcatc--cagtt-ttacccacttgcaaataactcctgt----acagGTATGCTAGAGAAGATACACACTATCTGTTGTATATGTATGACTTGATGAGGTTGAGACTGCAAAAGGAGTC---GACATCTGACAATGATCTTCTTCTAGAG
upper sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 6
---------------------------------cttgttta-tcttggttttagc-ttgatgattactg-gcacactgtcatgggcaat--ctaattagtaattattacaatctaattaactgtttttgtgatgacagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA
|||| | | ||| ||| | ||| ||| || | ||| | | || | | || | | || ||| | | | || || || ||||| |||||||||||||||||||||||||| ||||| ||||||||||| ||
gtattgtgcatataccctattctgaatttcttttctgttgactgttgagtttggtgttggatatttttgtgtttgctgcttttattttttgctggcttgccatcagttatatataagtggatttacttctgcc--tagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA---------------------------------------
upper sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 6
-cttgtttatcttggttttagcttgatgattactggcacactgtcatgggcaat-ctaattagtaattattacaatctaattaactgtttttgtgatgacagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA-
||| ||||| || || | | ||| || || | | | | | || | | | || | | || ||| | || | || || ||| ||||| |||||||||||||||||||||||||| ||||| || |||||||| | || ||| || | || | ||| ||| |
tcttttttattgtgtttggtgttggatattttttgtttgcttcttttctttatttctgacttgccatcagttatatataagtggctttacttctgcc--cagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAGACAGAGACTACAGAGGGAGTC-AACATTTGAAAATGATCTTCTTCTAGAG
upper sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G118917_T02 (Zea mays), 3'ss of exon 6
--------------------------------cttgtttatcttggttttagcttgatgattactggcacactgtcatgggcaatctaattagtaattattac--aatctaattaactgtttttgtgatg-acagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA-
| ||||| | | ||| || || ||| | ||| | | | | | ||||| || | | || | | ||| ||| || ||||||||| ||||| ||||||||||||||| | |||||||| ||| | ||||| | | || | ||| | || || | ||| | | |
gtactgtgcattgatactctgtccattgatttcatgtttgtttaatatttctttttatcattttccattttccgtcctc----acccagagaataatttccaccaagtgtatctcattgtgattgctgtgtgcagATATGCTAGAGAGGATACACACTATCTGCTATATATATATGACCTGATGAGATTGAGACTAGTGAATGGGTC-ATCATGTGAAAATGATCTTCTTTTAGAG
upper sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0056g01320.t01 (Vitis vinifera), 3'ss of exon 5
cttgtttatcttggttttagcttgatgattactggcacactgtcatgg-gcaatctaattagtaattatta-caatctaattaactgtttttgtgatgacagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA---
|| | | |||| | ||| | | | | | | | || ||| | || | | | ||| | || | | |||| ||||||||||||||| || ||||||||||||||| | || ||||||| || |||||||| | | || | | || || ||| || | |||| | ||
gttttctttcttcatgaattctttgttgtctcatgactattatgttgttgcaccttgatcctctgatctcatcaaattcttttatt--ttttatgatgacagATATGCTAGGGAAGATACACACTATTTACTGCATATATATGATTTAATGAGAACCCAATTGCTCTCAATGGCT---GAGCTGGAGAATTCTAATGCTCTTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggcaatctaattagtaattattacaatctaattaactgtttttgtgatgacagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA
aattaac putative branch site (score: 2)
tttttgt putative PPT
taattagtaattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgtttatcttggttttagcttgatgattactggcacactgtcatgggcaatctaattagtaattattacaatctaattaactgtttttgtgatgacagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - cttgatg
- - - - - - - - - - - - - - - - -ggcacac
- - - - - - - - - - - - - - - - - - - - tgtcatg