Sequence
atgc intronic sequence ATGC exonic sequencegttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttac-ctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
|| | | || | ||| || | |||| | || | | | |||| | || |||| | | || | || | |||||| | | | |||||||||||||||||||||||||| | ||||||||||| || || || || || || ||||||||||| ||||||||||| |||||||| ||||||||||| |
------------------------------------------gtaaaatgggtgt-taagttgtttgttgattgcacatatcgattttgttacactgtgtcctg--tttgactgtc-tggattgtt-------cattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttac-ctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
|| | | | | | ||| || | |||| | || | | | |||| | || |||| | | || | || | |||||| | | | |||||||||||||||||||||||||| | ||||||||||| || || || || || || ||||||||||| ||||||||||| |||||||| ||||||||||| |
------------------------------------------gtaaaatgggt-cttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctg--tttgactgtc-tggattgtt-------cattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
| | | | | || | || |||| | || || || | ||||| |||| || | || |||| ||| | | |||| || | | | ||||||||||||||||||||||| | |||||||||||||| ||||| || || || ||||||||||||||||||||||| || |||||||||||||| || |
---------------------------------------------------gtaagatgggtcctatgctgtt-tttat-tgattttactgtatt--ttgttaaattacatttatttgtcttggt-tatcgctaatcatttcttgtaccctttgatgt-atagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
||| | ||||| | | | | | | ||| ||||| | | | | | | | | || ||| | || | | ||||||||||||||||||||||||| | ||||||||||| || || || || || || ||||||||||||||||||||||| || |||||||||||||||| |
----------------------------------------------------------tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtg-----tgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC-----------------
||||| | | | | | | | | || ||| | || | | ||||||||||||||||||||||||| | ||||||||||| || || || || || || |||||||||||||| |||||||| || ||||||||||||||||| |
------------------------------------------------------------------------------------------------------caatttacattcacttatgtattgattgtttgctaagtgtg-----tgcacttttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
| | || || || | | | || || || | |||| | | || | || | | |||||| ||| | |||||||||| ||||| |||||| ||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||| |||||||||||||||| ||
--------------------------------------------------------------------------gtaatct--taaaatgaccattttcatttaaagtgtctcctatgggcttctttagt-atgctg--taacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
|||| | | | | | || | ||| || || | |||| || ||||| || || ||| || |||||||||| |||||||| ||| | ||||||||||||||||| | || |||||||||||||| || |||||||| || ||||||||||||||||| || |
-------------------------------------------------------------------gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtg------ttgtgacgat-------aaacctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 12
-gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgc--gtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccatt-gtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
||| |||| ||| | | || | | | | | | || ||| | || | ||| || ||| || || | | || ||||| || || | || || | | |||| || || | |||| | ||||| || |||||||||||| | ||| ||||| | |||||||| || ||||| ||||| ||||| ||||||||||| || ||||||||| | ||||||||||||| ||||
gtttgaaatgcaattggagat--gattattttttgtccacttaagacaattcttgttgggatgctaatttgagtttattt---tattatttttatcctgctaatttaaatgattttttttttta-aatataatt---ttgacattgaaaaccatgttttttttgtagACTGTGGATACTGACCTTGCACTCAAAATATATATTAAAGCGAGAGCAACTCCGAAAGTTGTTGCAGCCTTTGCTGAGCGTCGGGAGTTTGACAAAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
gattaat putative branch site (score: 3)
ttccatt putative PPT
tatatttgtgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT