Sequence
atgc intronic sequence ATGC exonic sequencegtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
Basic information
species | Glycine max |
transcript | GLYMA19G43410.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 3
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttt-tatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
| | | | | || || || | ||| | ||||| | | ||| | | ||| ||| | | ||| ||| | | |||| |||||||| ||||| |||||||||||||||| || ||| | |||||||| || | |||||| ||||| ||||||||||| |||| | ||||| |
-------gtttgtccatcaaaataattttaggctttagt---gttatgttttagtaaaaccagaagtt------gatttcctactgttttaactactgtccagCCTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 3
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttga--aaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
| ||| || | || || | | || | | | || || || || | || || |||| |||||||| ||||| |||||||||||||||| || ||| | |||||||| || | |||||| ||||| || |||||||| | || | ||||| |
--------------------gtgtgttcatcgaaatacaatgacgttcctgtttgttagacatatatacagtcaaatctaaatcccctcggtgttacgtttcagCCTCAAGATGCCTATGGCTTGGAGAAGCTTGCAACCGAGGAGCTGTGCAAGCACTACACCAAGGACTTTGGCATCGAGTGCCGCGTCGGCCGCTTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
|| | |||| || || | | |||| | || | || | | ||| ||| | ||| | ||| || | ||||||| |||||||| ||||| ||||||||||||| || || ||||| || |||||||| ||||| |||||||| |||||||| || ||||| || |||||||
-------------gtttgtgattatttttt--atatgttcttgctaaagatttatgagt-cttttctta--tgtgatgt-tttgatgctga------tatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EDP09235 (Chlamydomonas reinhardtii), 3'ss of exon 5
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatattt----gacttttt-----atagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
| || | ||| | | || | | || | | | || | | | | | | | || | || |||| |||||||| || || ||||||||||| || || || ||| | |||||||| || |||||||| || || ||||||||||| || | | | ||||| |
-----------gtcctctcggccgtgtgtctgcgtgtcgccggctgcttgctgcaccgcgacgccgctgtcactgctgattcttacacctcccaaacgtcttcgcccgcagCCCCAAGATGCGTACGGCCTGGAGAAGCTGGCCACCGAGGAGCTGTGCAAGCACTACAACAAGGACTTCGGCATTGAGTGCCGCATCGCGCGCTTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ10353 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaa--tacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
| | | || ||| | || || || |||| || | || | || | ||| |||| |||||||| ||||| ||||||||||| || |||||| | |||||||| || | |||||||||||| || |||||||| ||||| ||||||| |
--------------------------------gtatgaaaaagaaaaaaacaaaaaagcttcttttcttttgcgggga-atctgaaaaaatttgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTATGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37016 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgacttt-ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
| || | | | | | | | | || | | | || ||| || || |||| |||||||| ||||||||||||||||| || |||||| | |||||||| || | ||||||||||||||| ||||||||||||||| | ||||| |
-------------------------------------gtatgtgaaagaaagaaatcctttctttctgatctggaagttctaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACGGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ34003 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggtt---agcagggatatatttaatatttgacttt-ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
|| | | | || ||| || | | | | | | || ||| || || |||| |||||||| ||||||||||||||||| || |||||| | |||||||| || | |||||| |||||||| ||||||||||||||| | ||||| |
------------------------------------------gtatgtgaaagaagaaccctttctttctgatctgaaagttctaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACCGAAGAGCTGTGCAAGCACTACACCAAGGACTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ33664 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgacttt-ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
| || | | | | | | | | || | | | || ||| || || |||| |||||||| ||||||||||||||||| || |||||| | |||||||| || | ||||||||||||||| ||||||||||||||| | ||||| |
-------------------------------------gtatgtgaaagaaagaaatcctttctttctgatctggaagttctaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACCGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ37510 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggtt---agcagggatatatttaatatttgacttt-ttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
|| | | | || ||| || | | || | | | || ||| || || |||| |||||||| ||||||||||||||||| || |||||| | |||||||| || | ||||||||||||||| ||||||||||||||| | ||||| |
------------------------------------------gtatgtgaacgaagaaccctttctttctgatctggaagttgtaaaactcttgttttccttgcagCCCCAAGATGCCTATGGGCTGGAGAAGCTGTGCACCGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGGCGCTTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaa-tatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
|| | | | | || | ||| || ||| || | || | | | ||| |||| |||||||| ||||| ||||||||||| || |||||| | |||||||| || | |||||||||||| || |||||||| ||||| ||||||| |
---------------------------gtatgaaaaagaaaaaaaaaaaaaaaaaaggttcttttcttttgtggggaatctaaaaacaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ36458 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
||| | | | | || || || |||| || | | | ||| |||| |||||||| ||||| ||||||||||| || |||||| | |||||||| || | |||||||||||| || |||||||| ||||| ||||||| |
----------------------------------gtatgaaaacgaaaaaaaaaagcttcttttcttttgcggggaatctgaaaaaaaattgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatat-atttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
||| ||| | | |||| | | | || || | | ||| || | || ||| ||||| |||||||| ||||| || |||||||| | |||||| | |||||||| || | ||||||||||||||| |||||||||||||| ||||| || |
----------------------------------gtatgctgtcttccaagaaaaaaacaacttgtttctcaaactttttgtttttcatgttgctctttctagCCTCAAGATGCTTATGGACTAGAGAAGCTCTGCAGTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGAATCGAGTGCCGGATTGGAAGATTTCACA
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 2
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
| | | | ||| | ||| || ||| || | || | || | ||| |||| |||||||| ||||| ||||||||||| || |||||| | |||||||| || | |||||||||||| || |||||||| ||||| ||||||| |
------------------------------gtatgaaaaagaaaaaaaaaaaaaaaacttcttctcttttgtggggaatctgaaaaaatttgcactttgcagCCCCAAGATGCCTATGGACTGGAGAAGCTGTGCACTGAAGAGCTGTGCAAGCACTACACCAAGGATTTTGGGATCGAGTGCCGCATTGGACGATTCCACAMapped 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|209713688|gb|BW681841.1|BW681841EST: AGTTGGAGACAAATGTGAGTTTAAAGGAGTCTGATGCCTGGCCTGCTGAG CCACAAGATGCATATGGGCTGG
genomic: AGTTGGAGACAAATGTGAGTTTAAAGGAGTCTGATGCCTGGCCTGCTGAGgtttgttgct ... ctttttatagCCACAAGATGCATATGGGCTGG
EST:
gi|15287506|gb|BI471397.1|BI471397EST: AGTTGGAGACAAATGTGAGTTTGAAGGAGTCTGATGCCTGGCCTGCTGAG CCACAAGATGCATATGGGCTG
genomic: AGTTGGAGACAAATGTGAGTTTAAAGGAGTCTGATGCCTGGCCTGCTGAGgtttgttgct ... ctttttatagCCACAAGATGCATATGGGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
atttgac putative branch site (score: 4)
ctttttat CT-rich tract
atatatttaatatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT