Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaccctgatttcatgtttacgcttctagaatttcacaacagtaggacaaaaactagtttgatatgctgcagGTACTCAACATTTGTTAATTGGGAATTCTGGTGGCCAAACTTCCCTATCTTGGTTTACTTCAAGGAGACACAAACAAAGCCTGAGGGACAAATTCATTGC
Basic information
species | Glycine max |
transcript | GLYMA17G12380.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12380.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g33290.1 (Oryza sativa), 3'ss of exon 7
------------------gtaagtaccctgatttcatgttt----acgcttctagaatttcacaacagtag-gacaaaaactagtttgatatgct-gcagGTACTCAACATTTGTTAATTGGGAATTCTGGTGGCCAAACTTCCCTATCTTGGTTTACTTCAAGGAGACACAAACAAAGCCTGAGGGACAAATTCATTGC
|| | | | || || | | | | || | |||||||| | || || || | |||||||||||||||||| ||||||||| | ||||||||| | || |||||||||||||| ||||||||||| |||||||| || || || |||||||||| |
aaacatgtcgatcacgcgccaaaggtcgggctatcttgctcgataaatcgctttgatcatggtaacagtagtaatgcctgataattgaatgcacccacagGTACTCAACATTTGTGAATTGGGAACTGTGGTGGCCACAATTTCCTATCTTGGTTTATTTCAAGGAGACCCAAACAAAACCCGAAGGGCAAATTCATTTC
upper sequence: GLYMA17G12380.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G088138_T05 (Zea mays), 3'ss of exon 5
--------------------------gtaagtaccctgatttcatgtttacgcttct-----agaatttcacaacagtaggacaaaaac----tagtttgatatgc-tgcagGTACTCAACATTTGTTAATTGGGAATTCTGGTGGCCAAACTTCCCTATCTTGGTTTACTTCAAGGAGACACAAACAAAGCCTGAGGGACAAATTCATTGC
| || || | ||||| ||| | || | || || | || || || | | || | ||||||||||| || || || ||||| | ||||||||| | || ||| |||||||||||||||||||||| ||||| ||||| || ||||| || || | |
gtacgcaggcggcctgttgatccttcacacgt-cctttttttcagttttgtgtatcatcatgataacttgataagagggggtttacgatctaataacccaaggcatgcatagGTACTCAACGTTCGTAAACTGGGAGCTGTGGTGGCCACAGTTTCCTGTCTTGGTTTACTTCAAGGAGACCCAAACGAAGCCCGAAGGACAGATCCACTTC
upper sequence: GLYMA17G12380.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv11s0016g05260.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtaccctgatttcatgtttacgcttctagaatttcacaacagtaggacaaaaactagtttgatatgctgcagGTACTCAACATTTGTTAATTGGGAATTCTGGTGGCCAAACTTCCCTATCTTGGTTTACTTCAAGGAGACACAAACAAAGCCTGAGGGACAAATTCATTGC
|| ||| | ||| |||| | ||| | | | | | || ||| || || | | | | ||| || |||||||| || || |||||| |||||||||| ||||||||||| ||||| || || |||||||||||||| | |||||| |||||| | || | |
gtgagtgc----attctgagttt-cctttcaaaattctgataaagatagttggttcacctattggctttattacagATATTCAACATTCGTGAACTGGGAACTCTGGTGGCCCAACTTCCCTATTTTGGTGTATTTTAAGGAGACACAAACTAGGCCTGAAGGACAAGTGCACTTC
upper sequence: GLYMA17G12380.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ33300 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtaccctgatttcatgtttacgcttctagaatttcacaacagtaggacaaaaacta-gtttgatatgctgcagGTACTCAACATTTGTTAATTGGGAATTCTGGTGGCCAAACTTCCCTATCTTGGTTTACTTCAAGGAGACACAAACAAAGCCTGAGGGACAAATTCATTGC
|| || |||||| | | | ||| ||| | | ||||||||||| ||| || ||||| | |||||||||| ||| || ||| | || |||||||||||||||||||| ||||| ||||| ||| |||| |
---------------------gtaagcatctagaggaggaaagtcacggtctcttcactgtgttcttctttgtctagGTACTCAACCTTTACAAACTGGGAGCTATGGTGGCCAAGCTTTCCAATCCTCGTCTACTTCAAGGAGACACAAACCAAGCCGGAGGGCCAAGTTCACTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacgcttctagaatttcacaacagtaggacaaaaactagtttgatatgctgcagGTACTCAACATTTGTTAATTGGGAATTCTGGTGGCCAAACTTCCCTATCTTGGTTTACTTCAAGGAGACACAAACAAAGCCTGAGGGACAAATTCATTGC
gtttgat putative branch site (score: 5)
tagaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaccctgatttcatgtttacgcttctagaatttcacaacagtaggacaaaaactagtttgatatgctgcagGTACTCAACATTTGTTAATTGGGAATTCTGGTGGCCAAACTTCCCTATCTTGGTTTACTTCAAGGAGACACAAACAAAGCCTGAGGGACAAATTCATTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA