Sequence
atgc intronic sequence ATGC exonic sequencegtatattatctgtccctgatagactatgatagaaataatcttttaaactttaaaagagagattttggtgtagccattactcaagtttgtcgccattagtctatgaatgaagtatttcctttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACCATTACAAGAGATCTGCTGGGCA
Basic information
species | Glycine max |
transcript | GLYMA19G40050.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 16
gtatattatctgtccctgatagactatgatagaaataatc---ttttaaactttaaaagagagattttggtgtagccattactcaagtttgtcgccattagtctatgaatgaagtatttcctttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACCATTACAAGAGATCTGCTGGGCA
|| ||| | || | | |||| | |||| || ||| | ||| |||| | || | | || || | || | | | ||||||| |||||||||||||| | || |||||||||||||||||||| ||||||||||||||||||||||| || || || || ||||||| ||||| |
----------------------gctgtgaaataagttagtacgctttatattttagaacggag------gagtatttattatcacatttccttaagaaagaactccaaa---gacttctcatctttgatagATTGGTTGGCTCAATGCAATCCGTGAATGGCAAGAAGAGTTTGTTGGTAACATGAGTTCTAGGGAATTTGTTGATACTATCACCCGAGATCTTCTGGGAA
upper sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 15
gtatattat-ctgtccctgatagactatgatagaaataatcttttaaactttaaaagagagattttggtgtagccatt--actcaagtttgtc--gccattagtctatgaatgaagtatttcctttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACCATTACAAGAGATCTGCTGGGCA
|| ||| || | || || | || ||| ||| ||||||| ||||| | | || || | || ||| ||| ||| || ||| | | | ||| || ||||| | ||||||| |||||||||||||| | ||||||||||||||||||||||| || |||||||||||||||||||| || || || || ||||||| || || |
--gtactatactttatctaatcta--atcatacgaatg--cttttaagctttatagtat---ttctgctttacatattgtactgcagtgggtttgagaattttttttttaatagcataccatctttc--atagATTGGTTGGCTCAATGCAATCCGCGAGTGGCAAGAAGAGTTTGTTGGTAATATGAGTTCTAGGGAATTTGTTGATACTATCACCCGAGATCTTCTAGGAA
upper sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G416698_T01 (Zea mays), 3'ss of exon 9
gtatattatctgtccctgatagactatgatagaaataatcttttaaactttaaaagagagattttggtgtagccattactcaagtttgtcgccattagtctatgaatgaagtatttcctttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACCATTACAAGAGATCTGCTGGGCA
|| ||| | | | | || ||| || | |||||| | | | | | ||| | | | ||||| | | | || || || | | | | ||||||| |||||||||||||| | |||||||||||| |||||||||| || |||||||||||||
--gtactatacattatcta-atccaatcatactgatg--cctttaaagctaacagtactgctttaaatagtgtaccacaataggtttgagaaaaaaaattaat------agcataccatctttcatagATTGGTTGGCTCAATGCAATCCGCGAGTGGCAAGAAAAGTTTGTTGGTAATATGAGTTCTAGGG------------------------------------
upper sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv07s0005g00770.t01 (Vitis vinifera), 3'ss of exon 16
gtatattatctgtccctgatagactatgatagaaataatcttttaaactttaaaagagagattttggtgtagccattactcaagtttgtcgccattagtctatgaatgaagtatttcctttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACCATTACAAGAGATCTGCTGGGCA
| | |||| || ||| | | | || | || || | | | | || || | ||| ||| || |||||| |||||||||||||||| |||||||||||||| |||||||| || ||||||| || ||||||||||| ||||| | || | ||||||| | || |
------------------------------gtacttcatctgttgtccttcctgaattatgatagtcaacagtc-ttccttgaagggatttcgaataaatcattcaaagttcattctttttgctccagATTAGCTGGCTCAATGCAATCAGAGAGTGGCAAGAGGAGTTTGTCGGAAACATGACCTCCAGGGAATTTGTAGACACTGTCACTAAAGATCTGTTAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattactcaagtttgtcgccattagtctatgaatgaagtatttcctttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACCATTACAAGAGATCTGCTGGGCA
tatttcctttcctac CT-rich tract
aagtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattatctgtccctgatagactatgatagaaataatcttttaaactttaaaagagagattttggtgtagccattactcaagtttgtcgccattagtctatgaatgaagtatttcctttcctacagATTGGCTGGCTCAATGCAATTAGAGAGTGGCAAGAAGAGTTTGTTGGCAACATGAGTTCTAGGGAATTTGTCGACACCATTACAAGAGATCTGCTGGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC