Sequence
atgc intronic sequence ATGC exonic sequence...agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctgcaaaaatgttaaaatgcttttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
Basic information
species | Glycine max |
transcript | GLYMA08G19320.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 3'ss of exon 1
agtgaattagatttgaa-attgcggaattggttattaggtcgtgtttggtagtacgctgcaaaaatgttaaaatgcttttccttttg-tttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
| | | | |||||| |||| | | | | ||| || | | | | | | | ||||||| || |||||| || | ||||||||||||| || || |||||||| |||||||||| ||||||||||||||||||||||| |||||||| || || |||||||||||||| || |||
aattatgcacatttgattattgtttataggcctgcgatgtc-cattccacattcagtatttgttaagctgag-tgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 3'ss of exon 1
------agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctgcaaa-aatgttaaaatgcttttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
| | | |||||| ||| | ||| |||| ||| | || | || | | || | | || ||| | | ||| || || | ||||||||||||| || || |||||||| |||||||||| ||||||||||||||||||||||| |||||||| || || |||||||||||||| || |||
gcttctgattatgcacatttga--ttgtg---ttgtttat-aggcc-tgctatgtgctttccaataaccagtatttgttaaatttgtttcatatttcttatgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------------------agtgaattagatt-tg-aaattgcggaattggttattaggtcgtgtt--tggtagtacgctgcaaaaatgttaa----aatgcttttccttttg-tttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
|| | | ||| || | ||| ||| |||| | | | | | || | | |||||| | ||||||| || |||||| || | ||||||||||||| || || |||||||| |||||||||| ||||||||||||||||||||||| |||||||| || || |||||||||||||| || |||
gttttaaccattggtttgctgaatgtgtcttcagtgttgaaaaatttggacacatttgcttcaaattatgcacattcgactgttgtttataggcctgcgatgtccattccacattcagtatttgttaagctgactgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g26740.1 (Oryza sativa), 3'ss of exon 1
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttg-gtagtacgctg-caaaaatgttaaaatgcttttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
| | | ||| || | || ||| | | | | | ||| | | | | | | || | | | | || | | | |||||||||| || ||||| |||||||| ||||| |||| ||||| ||||||||||||||||| |||||||||||||| |||||||| || || ||||||
--taatctgatattgcaaataaggcattagaaagtgagcactatttatgcttaatgtcatctgtattcttgtagtattgaatatgttatcactgttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGGAAGCACACCCTACACAAGGTTACCCAGTACAAGAAAGGAAAGGATAGCC
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G160351_T01 (Zea mays), 3'ss of exon 1
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctgcaaa---aatgttaaaatgcttttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
| || | | ||||| | | | ||||| | || ||| | | | | | || | | ||| | ||||||||||||||||||| |||||||| ||||| |||| ||||| |||||||||||||||||||||||||||||||| |||||||| ||||| ||||||
-gggactaaaatttgttcatatattact--ttatttagcatgacttttcagtttattttatattgattctttgtggatgaattatgctgtacacatttcctagGTGAACGTTCCGAAAACCAAGAAGACCTACTGTAAGAACAAGGAATGCAGGAAGCACACCCTGCACAAGGTTACCCAGTACAAGAAAGGTAAGGATAGCC
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G009412_T01 (Zea mays), 3'ss of exon 1
agtgaattagatttgaaattgcggaattggttat---taggtcgt-gtttggtagtacgctgcaaaaatgttaaaatgctt----ttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
| | || | | | ||| |||| | |||| | ||| || ||||| |||| || || || |||| |||| | | ||||||||||||| || || |||||||| |||||||||| |||||||||| ||||||||| || ||||||||||| || |||||||||||||| ||||||
------tacagccccatatggagaacttgcttatgctttggtcttcagttgctaaggatatgcaattttgttttaacctttgcaatttctttcacatgttat--atagGTGAACGTTCCTAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAAGAAGCACACTCTCCACAAGGTTACTCAGTACAAGAAGGGTAAGGATAGCC
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G125527_T02 (Zea mays), 3'ss of exon 1
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgc-tgcaaaaatgttaaaa----tgcttttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
||| || |||| || | ||| | | | | | | || || |||| || ||| || ||| |||| | ||||||||||||||| || || |||||||| |||||||||| || ||||||| ||||||||| || |||||||| || || || |||||||| || ||||||
--tgaccctcata-gaaagtgttttttattcaattgactgctctctagagatggatatgaaatgttgttttaacatgtgcagtttgtttcacatgttat--acagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACACTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCC
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------agtgaattagatttgaaattgcgga--attggttattaggtcgtgtttggtagtacgctgcaaaaatgtta--aaatgcttttcc------ttttgtttgttg-------tgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
| | || | |||| | | | || |||| | | | | | || || | | | || ||||| | || | | ||||||| | | ||||||||||||| || || |||||||| |||||||||| || ||||||| |||||||||| | |||||||| || || || |||||||| || |||||||
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: AT4G14320.1 (Arabidopsis thaliana), 3'ss of exon 1
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggta--gtacgctgcaaaaatgttaaaatgcttttccttttg--tttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
| || | | || | || | | |||| || | ||| |||| ||| || || | ||| || ||| | |||||||| |||||||||| ||||| || |||||||||| |||||||||| |||||| ||| |||||||||| || || || ||||| ||||||||||||
----gttctgaagggcgtatttagattcacttctatgatcgtaattaattctgtatgctgttgaaactgtatcttgtggtagttttaaacttggttttctgtagGTGAACATTCCGAAAACTAAGAACACTTACTGCAAGAACAAGGAGTGCAAGAAGCATACCTTGCACAAGGTGACGCAGTATAAGAAAGGTAAAGATAGCC
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: AT3G23390.1 (Arabidopsis thaliana), 3'ss of exon 1
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctg----caaaaatgttaaaatgcttttccttttgtttgttg---tgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
| || || | || | || || || | | || ||| || | ||| | || || ||| ||| || | |||||||| |||| || |||||||| || ||||| |||| ||||| |||| ||||| || |||||||||||||||||||||||||||||||||| ||
---gttttcaatctaaa----tgatgtttgtattttgattaaccttaaaagtctcttgattttgtatgtgtgtgagtgattcatttttgattttatgaattttgaagGTGAACATTCCAAAGACAAAGAACACTTACTGTAAGAACAAGGAATGCAAAAAGCATACTTTGCACAAGGTTACCCAATACAAGAAGGGTAAAGACAGTC
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0064g00880.t01 (Vitis vinifera), 3'ss of exon 1
-----------agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctgcaaaaatgttaaaatgcttttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
|| ||| | || || | ||||| || | ||| | || | | | | |||| | | | | ||||||||||||||| || ||||||||||| ||||| ||||| |||||||| |||||||||||| |||||||||| || |||||||||||||| || ||||||
ggtgtaaaaagagcctgttatacttcggttttttagtcttgttatctggctttctttttcaatatgttttgttgaatatgaaatatatattgtctc-----------acagGTGAACGTTCCAAAGACAAAGAAGACGTACTGTAAGAGCAAGGAGTGTAGGAAGCACACCTTGCACAAGGTGACACAATACAAGAAGGGCAAGGATAGCT
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctgcaaaaatgttaaaatgcttttccttttgtttgttgtgaa-----cagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
||| | | | | | | | | | || |||| || | | || || || || | | ||| ||| |||| | |||||||| ||||| || |||||||||||||| || ||||| |||||||||||||||||||| |||||||||| || || |||||||||||||||||||||
-----atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctgcaaaaatgttaaaatgcttttcct-----tttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
| ||||| |||| | | || || | | ||| || | ||| | || || | | | ||| || | ||||||||||||||||||| |||||| | | ||| | |||| ||||| |||||||||||| |||||||| ||||| ||||||||||| || |||||
----tagtagatctgaa-tactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
upper sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S2_415V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------------agtgaattagatttgaaattgcggaattggttattag----gtcgtgtttggtagt----acgctgcaaaaatgttaaaatgcttttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
|||| || ||| || || || | | | | | || || ||||| | | | | | | || | | | | ||| || | || ||||||||||||||||||| |||||| | | ||| | ||| ||||| |||||||||||| |||||||| || || ||||||||||| || |||||
gttagcattccatccattccttctgctccggactcagtgcatttgttagttaggattatttcaaaggtgttacatcttcgatgctgctccttgtgatttggatgggacat-gcaatgtcagctgtgtgaatagttgtttttggcaattgttaggttttactgttgatgatcctcactgaggattgcatgatttgc-tagGTGAACGTTCCGAAAACGAAGAAGTCCTTCTGTCCTGGGAAGTCGTGCAAGAAGCACACCCTCCACAAGGTCACTCAGTACAAGAAGGGAAAGGATAGTCMapped 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|254338589|gb|GR845732.1|GR845732EST: GTCTGCTTCTTCCGATTCCGGCACGCCCCCATCACCATG GTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGG
genomic: GTCTGCTTCTTCCGATTCCGGCACGCCCCCATCACCATGgtaacattct ... ttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGG
EST:
gi|6666733|gb|AW278192.1|AW278192EST: GTCTGCTTCTTCCGATTCCGGCACGCCCCCATCACCATG GTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGG
genomic: GTCTGCTTCTTCCGATTCCGGCACGCCCCCATCACCATGgtaacattct ... ttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtagtacgctgcaaaaatgttaaaatgcttttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
cttttccttttgtttg CT-rich tract
aaaaatgttaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctgcaaaaatgttaaaatgcttttccttttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG