Sequence
atgc intronic sequence ATGC exonic sequence...ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
Basic information
species | Glycine max |
transcript | GLYMA19G04210.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 3
ttatccgaaaagggtccaagttaacagttgttctgagtttttagt-tcctactagcaagatccatcaacttagtttgacccattgctctgattta-tggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
| | | | | | | |||| | ||||| ||| | ||| || || || | | | | | | | | | | | | || | ||||||||||||||||| || |||||||| ||||||||||||||||||| || || | || || || || || || || || || || || || ||||
taagcatcgtgatggcgttatgagaagttaaattatgttttaagtcttataccagaaatttctctttattgattcttaacaa--gataaactctacttgcagTGACATGGAATGTGACCTGCACATACTCACAATTTCTTGCTCAGAAGACTCCAACCTGTTGTGTATCTCTCTCGTCATTTTACAATGACACAATTGTGAA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 1
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgc-----tctgatttatg-gcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
||| | | || | | || |||| | || | | ||| | || | ||| | |||| | | | | || | | ||||||||||||||||| || |||||||| || |||||||||||||||| || || ||||| || || || ||||| || ||||| || || ||||
--atc--atagtggctccatatagaagttaaattt-gtcaaaatcttatacca-taaagttcatttttgttttttgtttcttaacaaaaataaaatctgtttgcagTGACATGGAATGTGACCTGCACATACTCCCAATTTCTTGCTCAGAAGACTCCTTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
||| || |||| || | || || ||| | | |||| || || ||| || ||||||| |||||||| |||||||||||||| || ||| ||||||| ||| | || | ||| || || || |||||||| || || || || || | ||
----------------------gtaagtcatttcagtgttttttgtctttctggcg-------tcacaattatgacaccctttcttcctttttttg-cagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g41310.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------ttatccgaaaagggtccaagtta--acagttg-ttctgagt--ttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
|| || || | ||| || || | ||| || | || | ||| | | | | | | ||||| ||| | | ||| || |||||||||||||||| || |||||||||||||| || | || || ||| | || | |||||||| ||||| || ||||| || || ||||| | ||
gtaagatttttttctgaagtttccatgatcttagtatttgccgtgcaaagtagttcagggatgagcttacaatctattgcaacagattcagaattgttcttgtttcgatactgccttttcgtgcatcatcggtgaccgcttgatttcttttgtg-cagTGACATGGAATGTGACTTGCACATATTCACAGATTGTCGCGCAAAGATCTCCGACGTGCTGCGTTTCGCTCTCGTCTTTTTACAATGATACCATAGTTAA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G009154_T01 (Zea mays), 3'ss of exon 2
--ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
|| | | | ||| || || | | |||| |||| ||| | | | || || | | || ||||||||||||||||| || ||||||||||| |||||||||||||||| || | ||||| || || || ||||| || ||||| || || ||||
ttctaatcacagatagtcttaggaaaatttccatacaagttgc-agttttgtcta-tattttatagcattgagagttcttatcagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCTGTCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 3
--ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatg-gcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
|| | | | ||| || || | | |||| |||| | ||| | | | || || || | | | | ||||| ||||||||||||||||| || ||||||||||| |||||||||||||||| || || ||||| || || || ||||| || ||||| || || ||||
ttctaatcacagatagtcttaggaaaatttccatacaagttgc-agtttcgtcta-tattttatagca-ctgagggttcttaacagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 3
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatg-gcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
|| || | | |||| || | | | | |||| | || |||| | ||| || | | ||||| ||||||||||||||||| || ||||||||||| |||||||||||||||| || || ||||| || || ||
ctaatcgcagatagtcctaggaagaattccatacaagttgc-acttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCT------------------------------
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 3
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatg-gcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
|| || | | |||| || | | | | |||| | || |||| | ||| || | | ||||| ||||||||||||||||| || ||||||||||| |||||||||||||||| || || ||||| || || || ||||| || ||||| || || ||||
ctaatcgcagatagtcctaggaagaattccatacaagttgc-acttttgtctagattttatagcagagagggttcttaacagagacattctttatctgcagTGACATGGAATGTGACCTGCACATATTCCCAATTTCTTGCTCAGAAGACTCCATCCTGCTGTGTATCTCTATCATCGTTTTATAATGACACAATTGTGAA
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
ttatccgaaaagggtccaagttaacagttgttctgagtt---tttagttcctactagcaagatccatcaacttagtttgacccattgctctgat-ttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
| || || | | | | | | ||| | | || | || | |||| ||||| | || | | | | || ||||||| ||||||||||| |||||||| || || || | ||||||| |||||| | |||||| || || |||||||| || |||||| | || | || |
------gtaagttactcagttcttgaactctaccaaaacaaatttgacttttg--agtgaaatgaa--aactgagttttggcttttctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 3
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatca-acttagtttgacccattgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
| ||| | | || | | | || ||| ||| | | | | | | | | ||| | | || ||| |||||||||||| |||||||| || ||||| ||||||||||| || ||||||| || || | || || ||||| | ||||| |||||||| | ||| | ||| |
-aggatggcaagacacattgacaatggataatttgtgttcttaatatgcatttaaagagttctcaagatttaactaatctaatcttcctgtcctatggcagTGACTTGGAATGTTACTTGCACGTATTCACAATTCCTGGCTCAGAAGACGCCTACATGTTGTGTCTCATTGTCATCGTTCTATAATAACACTATAGTATC
upper sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 3
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgaccca--ttgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
| | | ||| || |||| | | ||| | | | |||| || || | | | | || | | | || |||||||||||||||| |||||||| ||||||||||| || |||||| ||| |||| |||||| |||||||| ||||||||||| || || || |||||||
--agggagtgattcttaaaggcaatttttgtcttccctaattaaaaatttgagctattacccataaatgtactgggcctaaacttatttctctctgtgacagTGACATGGAATGTTACATGCACGTATTCACAATTCCTGTCTCAGAAAACCCCCACTTGCTGTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctactagcaagatccatcaacttagtttgacccattgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
ctctgat putative branch site (score: 4)
tgatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - ctgagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctctg