Sequence
atgc intronic sequence ATGC exonic sequencegtaactcattttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA
Basic information
species | Glycine max |
transcript | GLYMA19G39780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038606_T03 (Zea mays), 3'ss of exon 2
--------gtaa---ctcatt-----ttttcattctctattttctttgatttctaacttattattattattactatga--tatgatgatggtgatggtgatgatgtaa---cagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA-
|||| | | || | ||| ||| | | |||| ||| | | || || | | | ||| | | || | ||| | ||| | ||||| ||||| ||||| |||||||| ||||||||| |||| |||||||| || ||||||||||||||||| | || || ||||| || || ||
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatctcagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAGG
upper sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 2
--------gtaa---ctcatt-----ttttcattctctattttctttgatttctaacttattattattattactat--gatatgatgatggtgatggtgatgatgtaa---cagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA
|||| | | || | ||| ||| | | |||| ||| | | || || | | | ||| | | || | ||| | ||| | ||||| ||||| ||||| |||||||| ||||||||| |||| |||||||| || ||||||||||||||||| | || || ||||| || || ||
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatctcagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAG
upper sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G095114_T01 (Zea mays), 3'ss of exon 2
---------------gtaactcattttttcattctctattttctttgatttctaactta--ttattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA
| || ||| || | | | | | ||||| | | | |||| || | || | ||| | | | || | ||| | ||||| ||||| ||||| ||||| || ||||||||| |||| |||||||| || |||||||||||||| || | || || ||||| || || ||
gtaagatcccggtgtctggcttctttcgtcgtcgtttttggcgtgtgattattcgttcagtctattgtttatcctgagtcctgaccgttaaaactttt-tgtgttctcagCTCGTGGAGCTGAAGAATGGTGAGACGTACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCACCTTAGGGAGGTTATTTGCACCTCAAAG
upper sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------gtaactcattttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA
|| | | ||| | | ||| || | ||||| | || | ||||| | || | || | || || | | || | ||||| || || ||||| |||||||| || ||||||||||| ||||| ||||| ||||||||||||||||| || |||||||| |||||||| ||
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaac-ttccttttactgtaattt-----tgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
upper sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
---------gtaactc-attttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgat-gtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA
|| || ||| ||| ||| ||| || || | | | || | ||| ||| |||| | || || || || || || ||||||||||| |||||||||||||| || || || || ||||| || ||||| ||||||||||||||||||||||| || |||||||| || || || |||
acatatagcataggtctattattttcctcttcttttcctctggtg---agatggctaggtattttagtat-atattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA
upper sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
------------gtaactcattttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA
|| | || ||||||||| | || | | | | | || | | | || || | || ||| ||| | |||||||||| || |||||||| || || || || |||||||||||||| || ||||| ||||||||||| ||||| || ||||| || ||||| || |||
cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcacttcgtgacctgtaactt----atactgcttgt-atgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA
upper sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S36_327V6.2 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------------------------------------------gtaactcattttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA
|| || | | || | | | || | | | ||| || | | | | | ||| | | | || | ||| | || || || |||||||| ||||| |||||||| ||||| || || || ||||||||||||||||| || || || ||||| ||||| || || ||
gtacgggtcacctttgccataacacttcttgaatatattctttggaacatcatgagaaaagatagaatttcacataatgcgaggagttgttgtgcacgactgtaatcattttatatcctgcatgttggatcgttacatggatcttttaggtctaac-atgacctcgtcggtaatctg-cagCTTGTCGAGCTCAAAAATGGAGAGACTTATAACGGCCATTTAGTAAACTGTGATACATGGATGAACATTCACCTACGTGAAGTTATTTGCACCTCAAAG
upper sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10085 (Selaginella moellendorffii), 3'ss of exon 1
gtaactcattttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA-
| | | | || || | | | || | | | | ||| | | ||||| || || ||||| ||||| || || ||||||||||| | ||||||| ||||||||||||||||| |||||||| ||||| || || ||
----------------------------------------gtgagtgatgttcttcgtttccttctttgtctgaaaattcgcttgggtagC---TAGTGGAGCTCAAGAATGGAGAGACTTACAATGGGCATTTGGTGAGCTGCGATAGCTGGATGAACATCCATCTACGAGAAGTTATTTGCACTTCCAAGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|15286667|gb|BI470558.1|BI470558EST: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgtaactcatt ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST:
gi|9259879|gb|BE348026.1|BE348026EST: CCAAGGCCACCCTATG TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CCAAGGCCACCCTATGgtaactcatt ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttattattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA
ttctaac putative branch site (score: 1)
attattattattacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactcattttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT