Sequence
atgc intronic sequence ATGC exonic sequence...acagataagcatccttggattttgttctaatgaggtttttaaccagttattgctatgattcttgttaaagatgtaatctaatgagatgctcatctttaggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT
Basic information
species | Glycine max |
transcript | GLYMA18G04730.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G126038_T01 (Zea mays), 3'ss of exon 1
---acagataagcatccttgga---ttttgttctaatgaggtttttaaccagttattgctatgattcttgttaaagatgtaatctaatgagatgctcatctttaggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT
|| | || ||||| | | | | | | ||| ||| || || | || | || | | | | |||| ||||||||||| |||||||| |||| || |||||||||||||| || || || || |||||||| || ||||||| |||||| | || |||||||| |||||
cataccatcagaaatgtttggagaaactagatacctcaaattgatgtacc--ttaggtctgtggatttttggagcactgagttatcact-gttgctgga--ttagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTGTCATGGAGTTCTTGCTGATGAACCATCCACTCGACTGCCCAATCTGTGA-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G145854_T01 (Zea mays), 3'ss of exon 1
acagataagcatccttggattttgttctaatgaggtttttaacc--agttattgctatgattcttgttaaagatgta--atctaatgag-atgctcatct--ttaggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT
| | || | ||| | | | | || | | || || | || || || | | ||||| || || |||||||||||||| ||||| |||| || ||||| |||||||| || || || || |||||||| || ||||||| |||||| | || |||||||| |||||
------ccataccattcaaaattggttggagaaactagatacctcaaattgatgtacctgaattagtgaattttggagcactgaatgatcattcttgctgaattagGGATGAAAATCAAGACAAACACCCCAGTGGCGAAGAAGGCGAGGGAGGGTGTCATGGAGTTCTTGCTGATGAACCATCCACTGGACTGCCCAATCTGTGA-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
acagataagcatccttgga---ttttgttctaatgaggt--ttttaaccagttattgctatgattcttgttaaagatgtaatctaatgagatgctcatctt-taggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT
| | ||| | | || | | || ||| | |||| | | | |||| | || | | | || | | | | | | | ||||||||| ||||||||||| ||||| | || |||||||| || || ||||||||||||||||| ||||||||||| || || ||||| || ||||||||
gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 1
acagataagc-atccttggattttgttctaatgaggtttttaaccag--ttattgctatgattcttgttaaagatgtaatctaatgagatgctcatctttaggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT
| || ||| | | | | || | | | ||||| | ||||| ||| | | || | | | | | |||||||||||| |||||||| ||||| || ||||| ||||| ||||||||||| ||||||||| | ||||||||||||| || ||||| |||||||||||
ttggctagatgatctgtatgcagcactatgttattcattctggcttggattatttttttgattgttg--acatattagggttttttttttttttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S28_321V6.2 (Physcomitrella patens), 3'ss of exon 1
-----------------------------acagataagcatccttggattttgttctaatgaggtttttaaccagttattgctatgattcttgttaaagatgtaatctaatgagatgctcatc----tttaggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT
| | || | |||| | || ||| | || || | || ||| | | ||| || | | | ||| |||||||| ||||| ||||||||| |||| ||||| || || || |||||||||||||| | ||||||| || || |||||||| || ||||| ||
gttcgattccgcgaaactagaagctgttttttgttggtttcccgcaaacattgtgtggagga--tttctggttggtagaatggattgtgtgtggcaaaagaagggggtgctaagaggcggagcggattccagGTATGAAAATCAAGACGGACACACCTCTGGCTAAGAAAGCAAGGGAGGGAGTGATGGAGTTCCTTCTGATGAACCACCCCTTAGATTGTCCGATTTGCGA-
upper sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S170_67V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------acagataagcatccttggattttgttctaatgaggtttttaaccagttattgctatgattcttgttaaagatgtaatctaatgagatgctcatctttaggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT
| |||| | || ||| | || |||| | | | | | | | | | || |||| | | |||| |||||||||||||| | |||||| |||| ||||| || || || ||||||||||||||||| |||||||| |||||||| |||||||| ||||| ||
gtctgattccattagttagtaaccctcttttctcagttgcaagctgtttgacatacaattcgtgcggttcttataacttggggtgtgtctaaaagcgggatactaagaggtcgaatggctgaattgcgtatagGTATGAAAATTAAGACCGGTACACCTCTGGCTAAGAAAGCAAGGGAGGGAGTGATGGAGTTTTTGTTGATGAACCATCCATTGGATTGCCCGATTTGCGA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttattgctatgattcttgttaaagatgtaatctaatgagatgctcatctttaggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT
atctaat putative branch site (score: 3)
ctcatcttt putative PPT
taatctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acagataagcatccttggattttgttctaatgaggtttttaaccagttattgctatgattcttgttaaagatgtaatctaatgagatgctcatctttaggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - gcatcct
- - - - - - - - - - - - - - - - - - - - - - - - - tgctatg