Sequence
atgc intronic sequence ATGC exonic sequencegtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
Basic information
species | Glycine max |
transcript | GLYMA20G19980.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gtatgcctacttgtgtcattttggttaatggtttatccctggt--gaacatcccactgaggttctgcaatggaaaaattgacatttaaaactgcccttt-tgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
| | | | ||| | | | | | | ||| | || | |||| ||| | || | | | || | | || || | ||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||| ||||| |||||||| || ||||| || || || |
--acacacaatgatgttgagaatggaagttgaattgcactgctaggagtggtgccctgaagttatattttg---acctgtatatgcatcatgacctttcctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 13
gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggt-tctgcaatggaaaaattgacatttaaaa---ctg---cccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
|| | | ||| ||| || || || |||| ||| |||| | | ||| || | ||| ||||||| || | | | ||||||| ||||| |||||||| || ||||||||||||||||||||||||||||||||| ||||||| || || ||||||||||||||||| || || || |
-agtggcggaacattctattactattactgatt-----ctagtgactgtcc---tgagttgtgagcatgggtattatttttttttaaaaaaattggatctttcctttagATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
-------------------------------gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgcaatgg---aaaaattgacatttaaaactgc--ccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
| ||| || | | ||| || || || | | | | | ||| || ||| || | || || ||| ||||| |||||||||||||||| ||||| ||||||||||||||||||||||||||||| |||||| | ||||| ||||| |||||||| || |||||||| || || |
gtgaggttattgacctactgtatgtatttacgaatggtagattacatgttcttgttttatatcgtaattgtaataactgttac-ctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
------------------gtatgcctacttgtgtca----ttttggtt--aatggtttatccctggtg-aacat-----cccactgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
||||| |||| || || || || || ||| | ||| || || | || || || || | | | || | || ||||| ||||||| ||||| || ||||| ||||||||||||||||||||||||||||| |||||| | ||||| ||||| |||||||| || ||||| || || || |
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcct--cctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
-----gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgc-aatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
||| ||| |||||| | | |||| | ||| || | | | | | |||| | ||| | | | | || |||| ||||||||||||| ||||| | |||||| |||| ||||| |||||||| || ||||| ||||||| ||||| || || ||||||||||| || || || |
gtaatgtacacct-cttgtgaacatcagactaataggctatt-------aatgcattattagtttattactaatgtcgagatt---actcata--tgggttttt--agATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgcaatggaaaaat-tgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
| ||| || || || | | || | ||| || |||| | | || | | || | | | || | | ||||||||||||| |||||||||||||||||||||||||| || |||||||| ||||| || ||||| ||||| || || || || ||||| || | || |
----gttagtccatgttataatgttttgggagt-----cttagaatcatagcagcctggttgta-agtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
-----------------gtatgcctacttgtgtcattt-----tgg---ttaatggtttatccc--tggtg-----aacatccca---ctgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
| | || |||| || ||| || ||| ||| | | | ||| | ||| || || | | | | || || | |||| || || |||||||||||||| ||||||| ||| ||| |||||||||| || | || ||||||||||| ||||| || || || ||||| ||||||||||| || ||||
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttcaagccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 11
gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
|| | ||| || || || | || ||| || | | |||||||||||| |||||||| ||||| ||||| ||||||||| | ||||| ||||| | ||||| || |||||||| || |||||||| || ||||| |
-----------------------------------------gtatgtacaccaaagac-ttttgtggcagcgtttttattattgtttcgcgcgcgagcgtagATTGGAGGAGGTAGTGAAGCGGAAGTCGGTGAAAAGAAGGATCGGGTGACCGATGCGCTGAATGCTACAAAGGCTGCAGTGGAGGAGGGAATCGTGCCAG
upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 11
gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
|| | ||| || || || | || ||| || | || |||||||||||| |||||||| ||||| |||| ||||||||| | ||||| ||||| | ||||| || |||||||| || |||||||| || ||||| |
-----------------------------------------gtacgtacgccaaagac-ttttgtggcagcgtttttattattgtttcgcgcgcgagtgtagATTGGAGGAGGTAGTGAAGCGGAAGTCAGTGAAAAGAAGGATCGGGTGACGGATGCGCTGAATGCTACAAAGGCTGCAGTGGAGGAGGGAATCGTGCCAGMapped 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|16279136|gb|BI943277.1|BI943277EST: GTTGCAGTGCTTAAG ATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACT
genomic: GTTGCAGTGCTTAAGgtatgcctac ... ccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACT
EST:
gi|19268755|gb|BM885011.1|BM885011EST: AGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAG ATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACT
genomic: AGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCAGTGCTTAAGgtatgcctac ... ccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcccactgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
aattgac putative branch site (score: 3)
ctgccctttt putative PPT
aaaaattgacatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG