Sequence
atgc intronic sequence ATGC exonic sequencegtgagttaaaccctcttttgctttatttttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaatactgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA
Basic information
species | Glycine max |
transcript | GLYMA10G02380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038606_T03 (Zea mays), 3'ss of exon 2
---gtgagttaaaccctcttttgctttatt--tttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaatactgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA-
|| ||| | | || || || || || | || ||||| | | | ||| || ||| | ||| || || | |||| ||| |||| || || | ||||| ||||| ||||| ||||| ||||| || |||||||| |||| ||||| || || ||||||||||| ||||| | || || ||||| ||||| ||
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattg---tta-gtcctgaccg-ttgaattgaaactattgtgatct-----cagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAGG
upper sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 2
---gtgagttaaaccctcttttgctttatt--tttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaatactgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA
|| ||| | | || || || || || | || ||||| | | | ||| || ||| | ||| || || | |||| ||| |||| || || | ||||| ||||| ||||| ||||| ||||| || |||||||| |||| ||||| || || ||||||||||| ||||| | || || ||||| ||||| ||
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattg---tta-gtcctgaccg-ttgaattgaaactattgtgatct-----cagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAG
upper sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagttaaaccct---cttttgctttatttttaccctcttttt-------ttagggttacgttattgttatat---gtatagaaattatgttaatactgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA
|||||| ||| | || | | |||| | | | | | ||| || | || || | || ||| | || | | || | || | | | || | || | |||| ||||| || || ||||| ||||| || || ||||| ||||| ||||||||||| ||||||||||| ||||| || |||||||| ||||| || ||
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
upper sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
gtgagttaaaccctcttttgctttatttttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaatactgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA
| | | | | |||| || |||||| |||| | | || | ||| ||| ||| | || || | || | || | |||| | |||||| ||| | ||||| |||||||||||||| ||||| || || || || || ||||||||||||||||||||||| ||||| || |||||||| || || || |||
-------acatatagcataggtctattattttcctcttcttttc--------ctctggtgagatggctaggtattttagta-ta-tattttacaagtca-ttgttat-tattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA
upper sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
gtgagttaaaccctcttttgctttatttttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaatactgcttgatttgtaacttgtg------acatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA
| || | || | | | | | || | ||| | ||| | ||| |||||||| | || |||| | || | ||||| || |||||||| || ||||| || ||||| |||||||| |||||||| ||||||||||||||||| || ||||| || |||||||| |||
-------------------------cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcacttcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
upper sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S36_327V6.2 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------gtgagttaa-accctcttttgctttatttttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaatac-tgcttgatttgtaact--tgtgacatatt--gtaa----cagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA
|||| || | ||| | | || | || | | | | | | |||||| | | || | ||| || | ||| || |||| | | |||| ||||| || || || |||||||| |||||||||||||| || || || || ||||||||||||||||||||||| || || ||||| ||||| ||||| ||
gtacgggtcacctttgccataacacttcttgaatatattctttggaacatcatgagaaaagatagaatttcacataatgcgaggagttgttgtgcacgactgtaatcattttatat-cctgcatgttggatcgttacatggatcttttaggtctaacatgacctcgtcggtaatctgcagCTTGTCGAGCTCAAAAATGGAGAGACTTATAACGGCCATTTAGTAAACTGTGATACATGGATGAACATTCACCTACGTGAAGTTATTTGCACCTCAAAG
upper sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10085 (Selaginella moellendorffii), 3'ss of exon 1
gtgagttaaaccctcttttgctttatttttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaat-actgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA-
| | ||||| | | | | ||||| || | | |||||||||| || || ||||| |||||||| || ||||| ||||| | || |||| ||||||||||| ||||| |||||||| ||||| || || ||
--------------------------------------------------------------------gtgagtgatgttcttcgtttccttctttgt--ctgaaaattcgcttgggtagCTAGTGGAGCTCAAGAATGGAGAGACTTACAATGGGCATTTGGTGAGCTGCGATAGCTGGATGAACATCCATCTACGAGAAGTTATTTGCACTTCCAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatagaaattatgttaatactgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA
ttgtaac putative branch site (score: 2)
aaattatgttaatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttaaaccctcttttgctttatttttaccctctttttttagggttacgttattgttatatgtatagaaattatgttaatactgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT