Sequence
atgc intronic sequence ATGC exonic sequencegttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
Basic information
species | Glycine max |
transcript | GLYMA11G35460.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
| || | | ||| || | ||| || | | || | | | || | | | | | ||| | || | ||||| || | | ||||||||||||| ||||||||||| | ||||||||||| || || || || || || ||||||||||| ||||||||||| |||||||| ||||||||||| |
-gtaaaatgggtgt-taagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtc---tggattgttcat--taattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
| || | | ||| || | ||| || | | || | | | || | | | | | ||| | || | ||||| || | | ||||||||||||| ||||||||||| | ||||||||||| || || || || || || ||||||||||| ||||||||||| |||||||| ||||||||||| |
-gtaaaatgggtct-taagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtc---tggattgttcat--taattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
|| | | | ||| || |||| || | | | |||| ||||| |||| || | || |||| ||| | | |||| | || | | | ||||||||||| ||||||||||| | |||||||||||||| ||||| || || || ||||||||||||||||||||||| || |||||||||||||| || |
gtaagatgggtcctatg---ctgtttttattgattttactgtat-------tttgttaaattacatttatttgtcttggt-tatcgctaatcatttcttgtaccctttgatgt-atagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
| | || | |||||| | | | | | ||| ||||| | | | | | | | | || ||| | | | | ||||||||||||| ||||||||||| | ||||||||||| || || || || || || ||||||||||||||||||||||| || |||||||||||||||| |
-------------tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgt-----gtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC-----------------
||||| | | | | | | | | || ||| | | | | ||||||||||||| ||||||||||| | ||||||||||| || || || || || || |||||||||||||| |||||||| || ||||||||||||||||| |
---------------------------------------------------------caatttacattcacttatgtattgattgtttgctaagtgt-----gtgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
| | || | | | || | | | || || || | |||| | | || | || | | |||||| ||| | |||||||||||||||| ||||| ||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||| |||||||||||||||| ||
-----------------------------gtaatcttaaaatg-accatt-ttcatttaaagtgtctcctatgggcttctttagt-atgctg--taacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
| | || | | || | | || || || || | |||| | ||| | ||||| | ||| ||| || ||||||||||||||||||| || | ||||||||||||||||| | || |||||||||||||| || |||||||| || ||||||||||||||||| || |
-----------------------------gtaatcttgaaatggacgatt--ttattcaaaatgtgtgatatgtc-tcctatggt-gtgttg--tgacgataaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 12
----------------------gttgggttgcattta--taattttgcttttgtttacctaatagtatactactgcttgttgaatttg--cttatta--tgaaatggtatatttgtgt-----taatttt--tattaa----tatgttccatt-gtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
|| || | | ||| | ||||| | || | | | || | | ||| | | || | ||||| | | ||| | | ||||||| ||| | ||||| || |||||||||||||| ||| ||||| | |||||||| || ||||| ||||| ||||| ||||||||||| || ||||||||| | ||||||||||||| ||||
gtttgaaatgcaattggagatgattattttttgtccacttaagacaattcttgttgggatgctaatttgagtttattttattatttttatcctgctaatttaaatgatttttttttttaaatataattttgacattgaaaaccatgttttttttgtagACTGTGGATACTGACCTTGCACTCAAAATATATATTAAAGCGAGAGCAACTCCGAAAGTTGTTGCAGCCTTTGCTGAGCGTCGGGAGTTTGACAAAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
tattaat putative branch site (score: 2)
ttccatt putative PPT
ttatgaaatggtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT