Sequence
atgc intronic sequence ATGC exonic sequence...tatcagatgatcagtaaagatgaggggtattttgctcatatatatttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT
Basic information
species | Glycine max |
transcript | GLYMA10G10180.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 10
-tatcagatgatcagtaaagatgaggggtattttgctcatatatatttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT
| ||| | | || || | || | || | || | | | || | | | || ||| || | | | || || |||||||| | |||||||||||||| || || || || || |||||||| ||||| ||||| || || ||||||||||||||||| || || ||||||
gctttttatgttacatttgagctagctgtgtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgc-atatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 12
----tatcagatgatcagtaaagatgaggggtattttgctcatatatatttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT
| | ||| | | || | || || | | || || ||| | | | || | | | | || | ||| ||| || ||||||||||| | ||||| || ||||| |||||||| ||||| |||||||| ||||| ||||| || || ||||| || || |||||||| |||||||||
ctctttataaatggttaacaattcctttcag-atcttatcgagaaattttagatccttttacttttcttat---tgtctattaacggtttgtttgtaatttcagAAAAATTGTTTTGGCAACCAACATTGCGGAGAGTAGTATCACTATAGATGATGTTGTCTATGTGATTGATTGTGGTAAGGCCAAGGAGACAAGCTATGAT
upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G119671_T01 (Zea mays), 3'ss of exon 3
----tatcagatgatcagtaaagatgaggggtattttgctcatatatatttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT
| | ||| | | || | || || | || || ||| | | | || | | | | || | ||| ||| || ||||||||||| | ||||| || ||||| |||||||| ||||| |||||||| ||||| ||||| || || ||||
ctctttataaatggttaacaattcctttcag-atcttatcgagtaattttagatccttttacttttcttat---tgtctattaacggtttgtttgtaatttcagAAAAATTGTTTTGGCAACCAACATTGCGGAGAGTAGTATCACTATAGATGATGTTGTCTATGTGATTGATTGTG--------------------------
upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 10
tatcagatgatcagtaaagatgaggggtattttgctcatatatatttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT
|| | | | | | || | || | | || | | || ||| | | | | |||| | | ||| |||||| |||||||||||||| ||||| ||||| |||||||| |||||||||||||| ||||| || |||||||||||||| || |||||||| || || || |||
--gcaagcatccttcatctactaag--ccttctatctattagtgatgcatctga--aacagattatttttcaattctaaattgctttgcatctattgtagGAAAATTGTGCTAGCCACAAACATTGCAGAGAGTAGTATCACCATAGATGATGTTGTATACGTCATAGACTGTGGAAAGGCAAAGGAAACAAGTTACGAT
upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ25900 (Selaginella moellendorffii), 3'ss of exon 7
tatcagatgatcagtaaagatgaggggtattttgctcatatatatttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT
| | | | | | | | ||| | || | || || ||||||||||| |||| || |||||||| || | |||||| || || ||||||||||||||||| || |||||||| ||||| ||||| || |||||||||
------------------------------------------------gtaatgcttccggctgatcgttttgatttctaactttctgctttcaatgcagAAAAATTGTCTTAGCGACGAATATTGCAGAAACTAGCATAACTATTGATGACGTTGTGTATGTTATCGACTGTGGGAAAGCTAAGGAAACTAGCTATGAT
upper sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ10915 (Selaginella moellendorffii), 3'ss of exon 10
tatcagatgatcagtaaagatgaggggtattttgctcatatatatttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT
| | | | | | | || | | | || | || || ||||||||||| |||| || |||||||| || | |||||| || || ||||||||||||||||| || |||||||| ||||| ||||| || |||||||||
------------------------------------------------gtaatgcttccggccgatcgtttgatttctaact-ttctgctttcaatgcagAAAAATTGTCTTAGCGACGAATATTGCAGAAACTAGCATAACTATTGATGACGTTGTGTATGTTATCGACTGTGGGAAAGCTAAGGAAACTAGCTATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT
ttttgat putative branch site (score: 4)
ttatttttct putative PPT
tatgttttgattgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatcagatgatcagtaaagatgaggggtattttgctcatatatatttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - tgagggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg