Sequence
atgc intronic sequence ATGC exonic sequence...tttttgtaattagaagtgaagacataaaacattttgttaaaccaagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
Basic information
species | Glycine max |
transcript | GLYMA14G37510.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
tttttgtaattagaagtgaagacataaaacattttgttaaaccaagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
|||| || | | || || || || | | | |||| ||| | | | | | | |||| | || ||| ||||||||||||| | |||||||||||| | | ||||| |||||||| ||||| ||||| ||||||||||| || ||||| |||| || |||||||
-----gtaa--agcgattagatgattgtactgcttattgatgttattttt-ccttttttttttattttgaataactaatggctggaatgcct-tgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
tttttgtaattagaagtgaagacataaaacattttgttaaaccaagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
|||| || | | || || || || | | | | || ||| | | | | | | |||| | || ||| ||||||||||||| | |||||||||||| | | ||||| |||||||| ||||| ||||| ||||||||||| || ||||| |||| || |||||||
-----gtaa--agcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctggaatgcct-tgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
--tttttgtaattagaagtgaagacataaaacattttgttaaacc------aagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
| ||| | | || | | ||||| | | || || ||| |||| ||||| | ||| || | || | | || |||| | ||||||||||| | |||||||||||| | ||||||| |||||||| ||||| ||||| || |||||||| ||||||||| | ||||| ||||| |
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgtttt-caatt--taattacctgtgttcatttct-tgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 3
------------------tttttgtaattagaagtgaagacataaaacattttgttaaaccaagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
| ||| | | | || | | | | | | ||||| ||| | || |||| | || || | | || | | | |||| ||||||||||||| | || ||||||||| | ||||||| |||||||| ||||| ||||| || |||||||| ||||||||| | ||||| ||||| |
gtacaaaatagccagataatcttgcagtgcctattgctgctgctgttgttgtaatcgtgcgatgcatattgttactgctttttaatt--taataacctgtgtccatttctg-gagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 11
tttttgtaat-tagaagtgaagacataaaacattttgttaaaccaagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
|||| || || | || | ||| || | | | || | || | || | ||| | | | |||| | | | || |||| ||||||||||||| | || ||||||||| | | || || |||||||| ||||| ||||| || |||||||||||||||||| | || || |||||||
-----gtaaaataaaaataaaatagccagaca----gtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgttaa---tttat-tgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 26
tttttgtaattagaagtgaagacataaaacattttgttaaaccaagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
| ||| || |||||||||| | | ||| ||| || || | | || ||| || || ||| ||||||| ||||||||||| |||||||||||| |||||||||| |||||||||||||| || |||||||| || |||||||| |||||||| |||||||
------------gtgagagagattgaatttattttgttaatgttggtaggcttcataagcagaacatgtac--ataagatctagtgatgcgtgtggacagGTTGAGAAACATGAGCTTCTGGAGATGAGGCGTATTGCTGCTTATATTTATAAGAAAGCAGGTAGATGGAAACAATCCATTGCATTGTCAAAGAAAGACA
upper sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 14
--------------------------tttttgtaattagaagtgaagacataaaacattttgttaaacca-agcat----agccttaaagtt-tgacaattagtgattggc--------tttaaca----atgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
||| || | || | |||| |||| ||| || | ||| || | |||||| |||| ||| ||| | ||| ||| || | | | | |||||||||||||| || ||||| || ||| | || |||| ||| ||||| ||||||| |||||| |||||||| || || | |||||||| || |||||||
gtaagttccgtagtcattgctaatcagtttaatactatcaatatcatccatatgtgtttttattagttcacaacatggaaagtgtcaaagttgtgacttttatgtatttcccaggtaaatttgacatgttatatttttttacagATTGAGAAGCACGAACTTCTGGAAATGCGTCGCGTTGGTGCGTACATCTATAAGAGAGCTGGCAGATGGAAACAATCTGTGGCTTTGTCCAAGAAAGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
ctttaac putative branch site (score: 3)
ttaaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttgtaattagaagtgaagacataaaacattttgttaaaccaagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - -aaaacatt
- - - - - - - - - - - - - - - - - - - - - caagcat
- - - - - - - - - - - - - - - - - - - - - - - - - gccttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgattg