Sequence
atgc intronic sequence ATGC exonic sequence...ataatattgacagggtgttttcactttccatggaatatatatatatttttggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
Basic information
species | Glycine max |
transcript | GLYMA14G14990.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
---ataatattgac-agggtgttttcactttccatggaatatatatatatttttggtagcattgctttgtgtactaaatt--ttagttg--------------ttt-------atattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
|||||| ||| | | | |||||| || | | ||||| | | | || ||| | || | | ||| || ||| || || |||||||||| |||||||| |||||||| |||| ||||| ||||| || |||||| |||||||| | ||||| || || ||| | ||||||||||| |||||||| |
gtactaatatcgaccatattatcttcactatctactcca-atatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
ataatattgacagggtgttttcactttccatggaatatatatatatttttggtagcattgctttgtgtact---aaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
|| | | | | | | | | || || ||||| | | | | ||| | | | || || || || | | |||||||| |||||||| |||||||| |||| ||||| ||||| || |||||| | |||||||| || | ||||| | | | ||||||||||| |||||||| |
--aacagatataagattcctgc-cattgaataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 3
ataatattgacagggtgttttcactttccatggaatat---atatatatttt-tggtagcattgctttgtg--tactaaattttagttgttt--atattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
| || || || | |||| | ||| | ||| | ||| || || | | ||| || | | ||| | |||||||| ||||| || || ||||| |||| ||||| ||||| || |||||||| |||||||| || || ||||| | | | ||||||||||| |||||||| |
--------catagaagattcataccacggaaggaacaccagatagttgctttgtacaagctttatcttctttttgttaacttattacagacacaatacgatcttgcagGGCATGTTCGTTCCAGCTATAAAAGGCCAAGGAACTGAGGAGCAGCAGCACAAGTGGTTACCACTGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
upper sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 2
ataatattgacagggtgttttcactttccatggaatatatatatatttttggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
| || ||| || | | |||| | || || | | | || | ||| || | | | ||||||||||||||||||| || ||||||||||||| || |||| || || ||||||||| || ||||| || |||||| |||||||| || ||||| |
----------------------gtataacacaaaatttacaatttcccttgggtggtttaattagaattttggtgttgaattggttttgtggtgg-atagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
tactaaa putative branch site (score: 1)
tattctttt putative PPT
tactaaattttagttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataatattgacagggtgttttcactttccatggaatatatatatatttttggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - gggtgtt
- - - - - - - - - - - - - -ccatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtac