Sequence
atgc intronic sequence ATGC exonic sequence...tatagcaattgcatgatgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
Basic information
species | Glycine max |
transcript | GLYMA19G45050.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 3
-tatagcaattgcatgatgacaccacacctatata-attccattcttgatt-tgcatttagttttc-tagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
| | || | ||| | | ||| || | || ||| ||| ||||| | | | | || || || ||| || | | | |||||||| |||||||| || |||||||| || || ||||| ||||||||||| |||||| ||||||||
attgttctgtttaacgattctagaagctttatctacagtcggttcctgacagtgcatgcaacctacatggttaatgg---cttccatttatatcaca-ccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
tatagcaattgcatg-atgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
|| || | | || | | || |||| | | | ||||| || || | || ||| | | || ||||||| |||||||| || || ||||| || |||||||| |||||||||||||||||| |||| |||
-gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgattta---tttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 3
-tatagcaattgcatgatgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
| | | | | | | ||| || || | | | | | | || | | | || | |||||||||| |||||||| || |||||||| || || ||||| ||||||||||| |||||| ||||||||
atttgcttgtcgagcaaaaaagtgcattttttatcataatgtttaacaaatctactagttcgcttcatacagtgactgcattatttacatcttta-tgcagGTTGTTGAGATCACAAAGGGAAGCAAAGTTAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 3
-tatagcaattgcatgatgacaccacacctatataattccattcttgatttgcatttagtt--ttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
| | | || | || | | ||||| | | || | || ||||| || | || | | | | || | | |||||||| |||||||| || |||||||| ||||| || || ||||||||||| |||||| ||||||||
ttgttgaggaaaaataagtgcatggtttttttttaattacgatatttaacaa-atctagttagctccaaacaatgaccgcgttatataatttttta--ttcagGTTGTTGAGATCACAAAGGGAAGCAAAGTCAAATACGAGCTTGACAAGAAAACTGGACTGATTAAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G026470_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------tatagcaattgcatgatgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttc-tgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG----------------------------------
| || || |||| |||| | ||| | | | || | | ||| | | | || | |||||| ||||||||||| || || |||||||| ||||| || || ||||||||||| || | || |||
gtaagtatctgacgaatcccattccccagacccctcaccccagcaagcaagcaagcaagcagccaaagttgttctcgatcgacat-gtgtgaatatggagcgtgtctgacgatccttccggtgcgcgtccgtccgtccgttacgtacgtggtgccgacgagcagGTCGTGGAGATCACCAAGGGGAGCAAGGTGAAGTACGAGCTGGACAAGAAGACGGGGCTCATCAAGGTGGACCGGATCCTCTACTCGTCCGTCGTCTACC
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
tatagcaattgcatgatgacaccacacctatataattccattcttgattt-gcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgc-agGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
| | |||| | |||| | | || | ||| | | | || | | || ||| | ||||||| |||||||||||||||||||||||||| || || |||||||| ||||| ||| | || |||
---------------gtaagttttttcctact---ctttgttctaaacagagtatgttgttattagattctctaatcattttatct-ttggatgattattagGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 2
tatagcaattgcatgatgacaccacacctatataattcc-attcttgatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
| || || ||| |||||| |||||| |||||| | | | | || | | |||||||||| ||||| || |||||||| || || |||||||| ||||||||||| ||||| ||||||||
---------------------gtatgccatcattcttctgattcttatccctcattta-ttttctgtcat-------tcatcgtctactcccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 3
tatagcaattgcatgatgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttct-gcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
| |||| | |||| | ||| | | | | | | | | || |||| | || | | | | ||| | | |||||||||| ||||||| | ||| |||||||| ||||| || ||||||||||||| || |||| |||
-gcccgtggggtgtgataatttcacagcagcatatcccgcagcacggctgggagtcatttagatagtcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 1
tatagcaattgcatgatgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
| | || | | | | || || || | ||| || ||| |||||| | ||||| ||||| ||| | ||||| ||||| ||||||||||| || |||||| ||| ||||||||| |||
------------------gttctggagctcccttagtttttaactg-cgtgagcttcatcctcttgttt---ggtagCATTGCTTGAATCGGTTTTCCAGGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAGAGTGGATTGATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
tcttgat putative branch site (score: 4)
atttagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatagcaattgcatgatgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - gcatgat
- - - - - - - - - - -ccacacc
- - - - - - - - - - - - - - - - - - -ccattct
- - - - - - - - - - - - - - - - - - - - - - - - -tgcattt