Sequence
atgc intronic sequence ATGC exonic sequence...atggtatctttgcatattctcagtttacatgcttctaacacagatgacttgtttgccttagagtataatataaaacttgcattaactgatgctcttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCGAAGCACATGTGGGCCAACATGATCCAATGGAGGAAAGAATATGGTACTGATACAATTATGGAG
Basic information
species | Glycine max |
transcript | GLYMA17G37150.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 3
atggtatctttgcatattctcagtttacatgcttctaacacagatgacttgtttgccttagagtataatataaaacttgcattaactgatgctcttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCGAAGCACATGTGGGCCAACATGATCCAATGGAGGAAAGAATATGGTACTGATACAATTATGGAG
| |||| | | || || | | | | || ||| | || | | ||||| | ||| |||| | || ||||| | |||||||||| |||||| ||||||||||| ||||| |||||| | ||||| | |||||||||| || || ||||| ||||||||| | |||
---------gtatatataccctatt-acttaccatcatttttt-taacccaactgc----aaacatgctg-atgacttg-actaattgat--ttgtgtagATTTCTAAAAGCAAGGAGATTTGACATTGAGAAAGCAAAGCAAATGTGGACTGACATGCTTAAATGGAGGAAGGAGTACGGTACAGATACAATTGTTGAG
upper sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G355610_T01 (Zea mays), 3'ss of exon 3
-------atggtatctttgcatattctcagtttacatgcttctaacacagatgacttgtttgccttagagtataatataaaacttgcattaactgatgctcttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCGAAGCACATGTGGGCCAACATGATCCAATGGAGGAAAGAATATGGTACTGATACAATTATGGAG
| | ||||| | || | || | | || | | | | || | | ||| | | || | ||| | ||| |||||||||| | |||||| ||||||||||| |||||||||| ||| | |||||| | ||||| | |||||||||| |||| || ||| | ||| |
gccacacacaaaa-ctttgtacatgtgc--ttgagaggccatgattggaagaaagtggtcgccatcctagttgactg---ggctgggattctcatttgca-ttgcagATTCCTAAAAGCACGGAAATTTGATGTTGAGAAAGCTAAGAATATGTGGTCAGACATGCTTAAATGGAGGAAGGAATTCGGGGTTGACAAAATAGAG---
upper sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 3
--atg-gtatctttgcatattctcagtttacatgcttctaacacagatgacttgtttgcctt-----agagtataa-tataaaacttgcat-taactgatgct--cttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCGAAGCACATGTGGGCCAACATGATCCAATGGAGGAAAGAATATGGTACTGATACAATTATGGAG
|| ||||| | | ||| | | | | | || | | |||| | || | | | || | | | || ||||| | || | ||||| | |||||||||||||||||||| || ||||| ||||| |||||| | ||| | || ||| ||| || ||||| |||||||| ||| |||||
gtatatgtatcca-gtaaattatgatgcaccttttgtttagcttgatgtgttagttttcatttttccaaatcacaagtgcacagctcaagcctaactaaatctggtctttagATTTCTAAAAGCAAGGAAATTTGATATCGACAAAGCAAAGCAAATGTGGATGGATATGCTTCATTGGCGGAGGGAGTATGGCACTGATACGATTTTGGAG
upper sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 2
atggtatctttgcatattctcagtttacatgcttctaacacagatgacttgtttgccttagagtataatataaaacttgcattaactgatgctcttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCGAAGCACATGTGGGCCAACATGATCCAATGGAGGAAAGAATATGGTACTGATACAATTATGGAG
|| | || | || || | || | | ||||| || | | | || || || | | || || | |||| |||||||||||||| |||||||||||||||| |||| | ||| |||||| || |||||| ||||||| ||||| | ||||||||| || ||| | |||
gtgagacttta------tttctgtcgattcatttttcatgatgatga--tgatggtgat-gatgatgattttgatgttctat------gttctctgttagATTCTTGAAAGCTAGGAAATTTGATATTGGGAAAACCAAGTTAATGTGGAGTAATATGATCAAATGGAGAAAAGATTTTGGTACTGACACCATTTTCGAG
upper sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 2
atggtatctttgcatattctcagtttacatgcttctaacacagatgacttgtttgccttagagtataatataaaacttgcattaactgatgctcttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCGAAGCACATGTGGGCCAACATGATCCAATGGAGGAAAGAATATGGTACTGATACAATTATGGAG
|||| || | | ||| | || | | |||| | | | |||| | || | || | || ||||||||| |||||||| ||||| |||||||| || || ||||||||||||||| || | ||||| || ||||||||| | | || || || || || |||||
-----gtcttacaatgctttgccttt-----ttcctgattttggctacttctctac---agagcttcat-------tctcagggattgccatctttgcagATTTTTGAAAGCCAGGAAGTTTGATATGGAAAAGGCGAAGCACATGTGGACCGAAATGATTCACTGGAGGAAAAACTTCGGCACCGACACTATCTTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacttgtttgccttagagtataatataaaacttgcattaactgatgctcttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCGAAGCACATGTGGGCCAACATGATCCAATGGAGGAAAGAATATGGTACTGATACAATTATGGAG
tgctctt CT-rich tract
tataatataaaacttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggtatctttgcatattctcagtttacatgcttctaacacagatgacttgtttgccttagagtataatataaaacttgcattaactgatgctcttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCGAAGCACATGTGGGCCAACATGATCCAATGGAGGAAAGAATATGGTACTGATACAATTATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - tgcatat
- - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - ctaacac
- - - - - - - - - - - - - - - - - - - - - - tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatta