Sequence
atgc intronic sequence ATGC exonic sequence...atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
Basic information
species | Glycine max |
transcript | GLYMA05G33420.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
atgaa-gtttggtgcatgcaat-----gatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
||| | |||||||| ||||||| | | || || ||| || || | | | | ||| | || ||| |||||||| || | ||| | |||||||||||||| ||| |||||| || |||||||||||||| || || ||| | || ||||||||||||||||| | ||
gtgagcaccaagaacatgcaatcactcgatgcttcctcat--aagcattgttg-atgaattattgtaacccaaaagtcttgatgaacctgctttatg-caatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G448834_T02 (Zea mays), 3'ss of exon 2
--------------atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
| || | ||| ||||| | || | | ||| || | | | || | |||||| || | ||| | || | ||||| ||||| | || | |||||||||||||| |||||||| | |||||| |||||||| || ||||| || | || ||||||||||||||||| | |||
gcaagtcaagtcggctccggtccattccatccaatgccaatgccaatatagtacatgtttatttatatatatg-ccatggttggtgga--tgatcatg---------catgcagGGGCGCTCGCGCGTCGGTGTGGGAGAACTTCAAGGACAACCCGCTGTTCGACATCTCGACGGAGCACCCGTCGACGTACTACGAGGACATGCAGCGCGCC
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G301552_T01 (Zea mays), 3'ss of exon 10
-------atgaagtttggtgcatgcaatgatgctttcata-acaaaacacacttggatcaaca-aataatcc-tggttgatgaaactgaccgt-gttttgca-atcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
|| | | |||| | ||| |||| | | || | | ||| || || | | | | ||| | | | || |||| | | |||||| || | ||| |||| ||||||||||| ||| |||| | ||| || |||||||| ||||| || ||| | ||||||||||| |||||||| |
gtaaatcatctatctgtctgcaagtgatgcagcttccctccactttttcccagtcattcatcacaacactgcgtccttggtctgatctctgatcattctgcatgttctacagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCGACTTACTACGAAGACATGCAGCATTCA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G000581_T01 (Zea mays), 3'ss of exon 3
-------atgaagtttggtgcatgcaatgatgctttc----ataacaaaacacactt------ggatcaacaa--ataatcctggttgatgaaactgacc-----gtgttttgca-atcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
|| | | |||| | ||| |||| | || | | ||| ||| | | || ||| | || |||| | || |||| | | |||||| || | ||| |||| ||||||||||| ||| |||| | ||| || |||||||| ||||| || ||| | ||||||||||| |||||||| | |
gtaaatcatctatctgtctgcaagtgatgcagcttccctctatgtccgcatcttctttttccccagtcattcatcacaacactgcgtcctgggtctgatctcttatcattctgcatgttctacagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCGACTTACTACGAAGACATGCAGCGTTCA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G141094_T02 (Zea mays), 3'ss of exon 2
-------atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaa--ataatcctggttgatgaaactgaccgt-----gttttgca-atcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
|| | | |||| | ||| |||| | | | | | ||| | | || || | | |||| | || |||| | | ||||| || | ||| |||| ||||||||||| ||| |||| | ||| || |||||||| ||||| || ||| | ||||||||||| |||||||| | |
gtaaatcatatatctatttgcaagtgatgcagcttccct--ccactttttccccagtcattcatcacaacattgtgtccttggtctgatctctgatcattctgcatgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
atgaagtttggtgcatgcaatg-atgctttcataacaaaacacacttgg--atcaa--caaataatcctggttgatgaaactgaccgtgt-tttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
| | | | | | | || || | | | ||||||| | | | || | |||| | ||||| | || || ||||| | || |||| |||| ||||| | ||| |||| ||||||||||| ||| |||| | ||| || |||||||| || || || ||| |||| ||||||||||||||||| | |||
--gtacgtcgctaccttcattgcacgtcctaataacaagccttgatgagccattgaatcaaagagtcctgat--gtgctacctaccgtatacttacaat---gcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 3
-------atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaaataatcct--ggttgat------gaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
|| | | | || |||||| | || | || |||| | | | | | | ||| || ||||| | || | | | |||||| || | ||| | || ||||||||||| ||| |||| | ||||||||||||||| || || || ||| | || |||||||| |||||||| | |
gtaattcatctatctgtctacaagcaatgcaattggcacctcgct-catttttggtcctcccactgcttcctgggtctattctctgatgactgatggcattgc-ctgttctacagAGGTGCTCGTGCATCGGTCTGGGAGAACTTCAAGAACAACCCGCTGTTTGACATCTCGACCGATCACCCACCAACATACTACGAAGACATGCAGCGCTCG
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G152029_T01 (Zea mays), 3'ss of exon 3
-------atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaa--ataatcctggttgatgaaactgaccgt-----gttttgca-atcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
|| | | |||| | ||| |||| | | | | | ||| | | || ||| | | |||| | || |||| | | |||||| || | ||| |||| ||||||||||| ||| |||| | ||| || |||||||| ||||| || ||| | ||||||||||| |||||| | | |
gtaaatcatctatctgtctgcaagtgatgcagcttccct--ccactttttccccagtcattcatcacaacactgcgtccttggtctgatctctgatcattctgcatgttctacagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCATCGACTTACTACGAAGACATGGAGCGTTCA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059845_T01 (Zea mays), 3'ss of exon 3
----------------------------------atgaagt--ttggtgcatgca--atgatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgttt--tgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
| | ||| || ||| ||| | || || | || ||| | | | | | || | |||| || || | |||| ||||| ||||| | || | |||||||||||||| ||| |||| |||||| |||||||| || ||||| || | || ||||||||||||||||| | |||
gtaccgtagtgctacgagcctgaactacctgacaaaggagtccttagtggatgaatcatcatcactgattagcaagtcttgac-gcacctgcgctgcgctgccgtgcgtataactaactgtatacgacgcaacaatgcagGGGCGCCCGTGCGTCGGTGTGGGAGAACTTCAAGAACAACGCGCTGTTCGACATCTCGACGGAGCACCCGCCGACGTACTACGAGGACATGCAGCGCGCC
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------------------------------atgaagtttggtgcatgcaat------gatgctttcataacaaaacacacttggatcaacaaataatcct---ggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
|| | ||| | ||| || | | || || | || || | | || | || | ||| || || | | | | ||| || ||||||||||| || ||||| ||||| || ||||||| ||||||||||||||| || ||||| ||||| || || || ||||||||||| |||||
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
--------atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgtttt---gcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
|| || | | ||||||| |||| ||| ||| || ||| || | || || |||| | |||| || | ||||||||||||| | ||||| ||||||||||| ||||| ||||||| || ||||||||||| || ||||| |||| ||||| || |||||||||||| | ||
attgttttttgttccttaatttgtccaatgat-ctttaatatgaaa-----tttatgccaa-----gatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
upper sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
----------atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
|| || || | |||| | | |||| ||| | | | | || | || ||| | | | || || | ||| | |||||| ||||| |||||||| |||||||||||||||||||| | ||| |||||||||||||||||||| ||||| || || || || ||||||||| | ||
aggaagcaacatcttgtatgatacatggctttgt-cttttatattaggtc-ctttgggttgaatgaatcaactcctat-------ctaactct-tttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCTMapped 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|13312605|gb|BG406256.1|BG406256EST: GGACTCTTTTATGATGTTGGCAATGACCCTGAAGGTGGTTACTATGCAAG AGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTG
genomic: GGACTCTTTTATGATGTTGGCAATGACCCTGAAGGTGGTTACTATGCAAGgtaggtctta ... aatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggatcaacaaataatcctggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
aactgac putative branch site (score: 2)
aacaaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - gcatgca
- - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - -aacacac
- - - - - - - - - - - - - - - - - - - - - - - - atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg