Sequence
atgc intronic sequence ATGC exonic sequence...atgtatatttatgttatatcatactgtcataaaactcataattagtttatcctcttaggccacataactaatggaggtgatcatttgtatttggtaacagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCCGACATTAAAAGAGGGAAGTTTTCCCAAGAAGAAGAACAAACAAT
Basic information
species | Glycine max |
transcript | GLYMA02G13770.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G13770.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g51799.1 (Oryza sativa), 3'ss of exon 1
----atgtatatttatgttatat--catac-tgtcataaaactcataattagtttatcctcttaggccac-ataacta-------atggaggtgatcatttgtatttggta------acagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCCGACATTAAAAGAGGGAAGTTTTCCCAAGAAGAAGAACAAACAAT
|||| || | || | ||| | | | | || || ||| | | | || | ||| || |||| | ||| || | ||| || |||| || |||||||||||||| || || ||| |||| |||||||||||| ||||||| ||||| || ||||| ||||| || | || | | || ||
gtatgtgtacatgcacaacggatggcgtacgtagctttgatcttgtagctagcatcgatccaaatgcagctatagctcgatggccatggcgttgagttttccttttttttacatgttgcagGGCTGAACAGGTGTGGCAAGAGCTGCAGGCTAAGATGGACGAACTACCTGAGGCCAGACATCAAGAGAGGAAAGTTCACCTCTGCCGAGAAGGATACCAT
upper sequence: GLYMA02G13770.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G159547_T01 (Zea mays), 3'ss of exon 1
-------------------atgtatatttatgttatatcatactgtcataaaactcataattagtttatcctcttaggccacataactaatggaggtgatc-atttgtatttggtaacagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCCGACATTAAAAGAGGGAAGTTTTCCCAAGAAGAAGAACAAACAAT
| | | || | | | | | | || || | | ||| ||| | |||| || | ||| || | | | | |||| ||||||||||||||||| || || ||| | || ||||| |||||||||||||| ||||| || ||||||||||| |||| || |||||||| || ||
gtacgtgactgccgggaacaaacctctccatttctctcggtctcggtgtgacgatgtaaaagaggtcgatcgctt---ccatgcgaa-aatgtagctcatcgatctagttgttattgcagGGCTCAACAGGTGTGGCAAGAGCTGCAGGCTGAGATGGACCAACTACTTGAGGCCAGACATCAAGAGAGGGAAGTTCACCCAGGAGGAAGAACAGACCAT
upper sequence: GLYMA02G13770.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g05670.t01 (Vitis vinifera), 3'ss of exon 1
atgtatatttatgttatatcatactgtcataaaactcataattagtttatcctcttaggccacataactaatggaggtgatcatttgtatttggtaacagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCCGACATTAAAAGAGGGAAGTTTTCCCAAGAAGAAGAACAAACAAT
| ||||||| | || || ||| | | || | | || || | || | | | || || || | |||| || ||||| ||||| || || |||||||| || |||||||| || || ||||| || ||||||||||| || ||||| |||||||||||||| |||||
------gtctatgttaattaattggatccct---ctccctgtct-ctcattttttcag--tacttcaccatttcatcatttcccttttactc--ctgcagGTCTTAACAGATGTGGAAAGAGCTGTAGGTTGAGATGGACGAATTATTTAAGGCCTGATATTAAAAGAGGAAAATTTTCTCAAGAAGAAGAACAGACAAT
upper sequence: GLYMA02G13770.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S2_55V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------atgtatatttatgttatatca-tactgt-cataaaactcat---aattagtttatcct---cttaggccacataactaatggaggtgat---catttgtatttggtaa---------cagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCCGACATTAAAAGAGGGAAGTTTTCCCAAGAAGAAGAACAAACAAT
| | | | | | | || || |||| || |||| | || | | || || | | | || || | | | | ||| | ||| |||| || | ||||||||||| || ||||| || || ||||||||||||||| |||||||||| || | || || ||| ||| || || || | ||
gtaggcatgaacctcttttttcttctaaaacttcaacaacgtcgtgcatagaagtcatctaagttcggtgatttcacatcggagcggcgcgattgatcgaatttaatggcgtgtgtgtatggctggaacatgtgcagGTCTGATGAGGTGTGGCAAGAGCTGTAGATTGAGATGGACGAACTACTTGCGGCCCGACATCAAGCGCGGCCGTTTCTCCGAAGCTGAGGATCAGATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatcctcttaggccacataactaatggaggtgatcatttgtatttggtaacagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCCGACATTAAAAGAGGGAAGTTTTCCCAAGAAGAAGAACAAACAAT
aactaat putative branch site (score: 2)
atttgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtatatttatgttatatcatactgtcataaaactcataattagtttatcctcttaggccacataactaatggaggtgatcatttgtatttggtaacagGACTCAACAGGTGTGGCAAAAGTTGTAGGTTAAGGTGGACGAACTACTTGAGGCCCGACATTAAAAGAGGGAAGTTTTCCCAAGAAGAAGAACAAACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - -tactgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaggtg