Sequence
atgc intronic sequence ATGC exonic sequence...taggagttattttatccctctaaccatgcctattaatggttgctagtgtttgtgaaatgaagatggataatcaatgttgttataatcttttgtctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
Basic information
species | Glycine max |
transcript | GLYMA07G38510.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 4
taggagt-tattttatccctctaaccatgcctattaatggttgctagtgtttgtgaaatgaa-gatggataatcaatgttgttataatcttttgtctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
| | || | | ||| || | | || | ||| ||||||| ||| || | | | | | | | || | || |||||||| ||||| ||||| |||||||| ||||||||||| || || || |||||||| ||||||||||||||||| ||||||||||| || |||||| | |
-aagtgtacacatgtattctccttttattttttgcatgggcttcta-tgtttgtccaatatccgaagcaccgatgaacataatgtgtttcattattttgcagTATACACCAGCAATAGATATATGGAGTATTGGCTGCATATTTGCCGAGCTTTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTG
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
--taggagttattttatccctctaacca-tgcctattaatggttgctagtgtttgtgaaatgaagatggataatcaatgttgttataatcttttgtctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
| || | | | | || | || |||| || || | || | | | || | || || | | || | |||| ||||| || ||||| ||||| ||||||||||| || ||||| || |||||||||||||| ||||||||||||||||| ||||| ||||| || |||||| | |
gcaatgaaatgctgtctagttccagttgctggctat--atttttctttgtacatataatgcctggagtatcggtgaaccttatactgttcaaat-tcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 4
taggagttattttatccctctaaccatgcctattaatggttgc-tagtgtttgtgaaatgaagatggataatcaatgttgttata---atcttttgtctttc--agTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
|| || || || | | | |||| || ||||||||||| | |||| | || || ||| | |||||| ||| ||||||| || || ||||| |||||||| |||||||| || || |||||| | ||||||||||||||||||||||| ||||| ||||| || |||||| | |
----gattgttgcatatttccttctcacctgttccatggccctgtatagtttgtgaaat--atctggagcaccattgaacaaatatgtgttttttgttttttgtagTATACACCGGCGATAGATATATGGAGTATTGGCTGTATATTTGCAGAATTGTTAACTGGAAAACCTCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 3
taggagttattttatccctctaa--ccatgcctattaatggttgc-tagtgtttgtgaaatgaagatggataatcaatgttgttataatcttttgtctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
| | |||| | | | | | | | || |||| | || | | || || | | ||||| | | | | || | || |||||||| ||||| ||||| |||||||| ||||| || || || || ||||| |||||||||||||| |||||||| ||||| ||||| || |||||| | |
--catgctcttttgttcataagaagcttcactcttgtataattgccttgtatagtttgttcgatatctgaggaatactgttga-acattgtgtttttttacagTATACACCAGCGATAGATATATGGAGTATTGGTTGTATATTTGCGGAACTATTAACTGGAAAACCGCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------taggagttattttatccctctaaccatgcctattaatggttgctagtgtttgtgaaatgaagatggataatc----aatgttgttataatcttttgtct---------ttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
| | | | | || || | | | | | | ||| | | | | | | | ||| | || | | ||| ||| |||||||||| || || ||||| ||||||||||| || |||||||| |||||||| ||||| || |||||||||||||| ||||| ||||| |||||||||||||
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
upper sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
-taggagttatttt--atccctctaaccatgcctattaatggttgctagtgtttgtgaaatgaagatggataatcaatgttgttataatcttttgtctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
| || | | | | ||| | || || || || | |||| || || | || || ||| | | ||| | ||| ||||||||||| ||||| ||||| |||||||||||||| ||||| || ||||| |||||||||||||||||||| || || || || |||||||| || |||||||
tcatgattcagtgtccatcatattgacaatagttaaccatact--ctag-gtatgatacctgtgatctgactgtcattttcgtttttgctctttcattttcagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtttgtgaaatgaagatggataatcaatgttgttataatcttttgtctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
tcttttgtctttc CT-rich tract
ttgttataatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taggagttattttatccctctaaccatgcctattaatggttgctagtgtttgtgaaatgaagatggataatcaatgttgttataatcttttgtctttcagTATACCCCAGCTATAGACATATGGAGCATTGGCTGCATTTTCGCAGAACTTTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - tccctct
- - - - - - - - - - - - catgcct
- - - - - - - - - - - - - - - - - - tggttgc
- - - - - - - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtt